{ "run": "2026-10-18", "outcomes": [ "valid", "unchecked", "invalid_json", "not_mvs", "invalid_mvs", "load_failed" ], "conditions": { "spec": { "claude-haiku-4-5": { "outcomes": { "valid": 67, "unchecked": 0, "invalid_json": 0, "not_mvs": 0, "invalid_mvs": 3, "load_failed": 0 }, "n": 70, "mvs_f1": 0.857, "failures": [ { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1xmi.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "res-myoglobin", "prompt": "Show me sperm whale myoglobin", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1mbn.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "focus", "params": {} } ] } ] } ] } ] } } }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1mwq.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } } ] }, "deepseek/deepseek-v3.2": { "outcomes": { "valid": 69, "unchecked": 0, "invalid_json": 0, "not_mvs": 0, "invalid_mvs": 0, "load_failed": 1 }, "n": 70, "mvs_f1": 0.9034, "failures": [ { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "load_failed", "load_error": "render failed: Error: FormatError\n at j_ (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7670:159)\n at Cwt (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7677:56875)\n at e.f (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7677:56472)\n at HJ (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:35:61538)\n at tG (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:35:60775)\n at lF.run (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7586:109461)\n at r4.runTask (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7586:123836)\n at tf (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7677:56495)\n at lY (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7675:29405)\n at e.loadMvsData (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7713:39371)", "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/3ptb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": { "label_comp_id": "BAM" }, "custom": { "molstar_show_non_covalent_interactions": true, "molstar_non_covalent_interactions_radius_ang": 5 } } } ] } ] } ] } ] } } } ] }, "deepseek/deepseek-v4-flash": { "outcomes": { "valid": 65, "unchecked": 0, "invalid_json": 4, "not_mvs": 0, "invalid_mvs": 1, "load_failed": 0 }, "n": 70, "mvs_f1": 0.8591, "failures": [ { "id": "gen-cartoon-1hho", "prompt": "Load haemoglobin (1HHO) and show the protein as a red cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 461 (char 460)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}]}" }, { "id": "gen-focus-1cbs", "prompt": "Load 1CBS; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 683 (char 682)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1cbs.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"grey\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}, {\"kind\": \"focus\"}]}]}]}]}]}]}" }, { "id": "grd-disulfide-1lyz", "prompt": "Load 1LYZ; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1176 (char 1175)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1lyz.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": [{\"auth_asym_id\": \"A\", \"auth_seq_id\": 6, \"auth_comp_id\": \"CYS\"}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 30, \"auth_comp_id\": \"CYS\"}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 64, \"auth_comp_id\": \"CYS\"}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 76, \"auth_comp_id\": \"CYS\"}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 80, \"auth_comp_id\": \"CYS\"}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 94, \"auth_comp_id\": \"CYS\"}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 115, \"auth_comp_id\": \"CYS\"}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 127, \"auth_comp_id\": \"CYS\"}]}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"yellow\"}}]}]}]}]}]}]}]}" }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 994 (char 993)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"I\",\"auth_seq_id\":57},{\"auth_asym_id\":\"I\",\"auth_seq_id\":102},{\"auth_asym_id\":\"I\",\"auth_seq_id\":195}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"}}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"green\",\"label_color\":\"green\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"I\",\"auth_seq_id\":195,\"label_atom_id\":\"OG\"},\"end\":{\"auth_asym_id\":\"I\",\"auth_seq_id\":57,\"label_atom_id\":\"NE2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}},{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"I\",\"auth_seq_id\":57,\"label_atom_id\":\"ND1" }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/5uak.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model", "model_index": 0 }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "focus", "params": {} } ] } ] } ] } ] } } } ] }, "gemini-3.5-flash": { "outcomes": { "valid": 66, "unchecked": 0, "invalid_json": 4, "not_mvs": 0, "invalid_mvs": 0, "load_failed": 0 }, "n": 70, "mvs_f1": 0.8486, "failures": [ { "id": "gen-range-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show residues 50-110 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 459 (char 458)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, \"{\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"beg_auth_seq_id\": 50, \"end_auth_seq_id\": 110}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}]}}" }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 184 (char 183)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1a6m.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\":" }, { "id": "int-002", "prompt": "Load 1A6M with the protein as a grey cartoon. Show the heme and the proximal histidine as ball-and-stick and measure the distance from the heme iron to the histidine's coordinating nitrogen.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 184 (char 183)", "raw": "Answering with only the JSON object, strictly matching the instructions:\n\n{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1a6m.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"" }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "JSON parse error: Expecting property name enclosed in double quotes: line 1 column 2 (char 1)", "raw": "\n ```\n Wait, `label_template` in the spec says `\"{{distance}}\"` is replaced. The example says `\"label_template\": \"{{distance}}\"`. Let's just use `\"{{distance}}\"` or `\"{{distance}} Å\"`. The spec example has `{{distance}}` and the text says `\"{{distance}}\" is replaced by it`. Let's use" } ] }, "google/gemma-3-27b-it": { "outcomes": { "valid": 57, "unchecked": 0, "invalid_json": 4, "not_mvs": 0, "invalid_mvs": 9, "load_failed": 0 }, "n": 70, "mvs_f1": 0.7133, "failures": [ { "id": "mvs-004", "prompt": "Load HIV-1 protease (1HVR); protein as grey cartoon, the bound inhibitor as magenta ball-and-stick, and focus the camera on the inhibitor.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 15 column 1 (char 850)", "raw": "\n```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hvr.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]},\n {\"kind\": \"focus\", \"params\": {\"radius\": 5}}]}]},\n {\"kind\": \"focus\", \"params\": {\"radius\": 5}}\n ]}]}]}\n]}}\n```" }, { "id": "hotspots-1tup", "prompt": "In p53 (PDB 1TUP), chain A, highlight the 6 mutational hotspot residues — the positions carrying the most pathogenic ClinVar variants — as red spheres.", "outcome": "invalid_mvs", "mvs_issues": [ "Invalid parameters for node of kind \"representation\":", " Invalid value for parameter \"type\":", " \"sphere\" is not a valid value for literal type (\"cartoon\" | \"backbone\" | \"ball_and_stick\" | \"line\" | \"spacefill\" | \"carbohydrate\" | \"surface\" | \"putty\")" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": [ { "auth_asym_id": "A", "auth_seq_id": 135 }, { "auth_asym_id": "A", "auth_seq_id": 136 }, { "auth_asym_id": "A", "auth_seq_id": 175 }, { "auth_asym_id": "A", "auth_seq_id": 248 }, { "auth_asym_id": "A", "auth_seq_id": 273 }, { "auth_asym_id": "A", "auth_seq_id": 307 } ] }, "children": [ { "kind": "representation", "params": { "type": "sphere", "size_factor": 0.4 }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] } ] } ] } ] } ] } } }, { "id": "gen-chain-1hho", "prompt": "Load 1HHO; show everything as a grey cartoon, then colour chain A red.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 12 column 1 (char 659)", "raw": "```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"all\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\"}}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}\n ]}]}]}\n]}}\n```" }, { "id": "gen-focus-1cbs", "prompt": "Load 1CBS; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1cbs.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 } } ] } ] } ] } ] } } }, { "id": "gen-focus-1hho", "prompt": "Load 1HHO; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1hho.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 } } ] } ] } ] } ] } } }, { "id": "gen-focus-2hhb", "prompt": "Load 2HHB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 18 column 3 (char 822)", "raw": "\n```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/2hhb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}\n ]},\n {\"kind\": \"focus\", \"params\": {\"radius\": 5}}\n ]}\n ]}\n ]}\n]}\n```" }, { "id": "gen-focus-3ptb", "prompt": "Load 3PTB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/3ptb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 5.0 } } ] } ] } ] } ] } } }, { "id": "gen-ions-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_mvs", "mvs_issues": [ "Invalid parameters for node of kind \"representation\":", " Invalid value for parameter \"type\":", " \"sphere\" is not a valid value for literal type (\"cartoon\" | \"backbone\" | \"ball_and_stick\" | \"line\" | \"spacefill\" | \"carbohydrate\" | \"surface\" | \"putty\")" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1hho.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ion" }, "children": [ { "kind": "representation", "params": { "type": "sphere" }, "children": [ { "kind": "color", "params": { "color": "purple" } } ] } ] } ] } ] } ] } ] } } }, { "id": "gen-ions-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_mvs", "mvs_issues": [ "Invalid parameters for node of kind \"representation\":", " Invalid value for parameter \"type\":", " \"sphere\" is not a valid value for literal type (\"cartoon\" | \"backbone\" | \"ball_and_stick\" | \"line\" | \"spacefill\" | \"carbohydrate\" | \"surface\" | \"putty\")" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/3ptb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ion" }, "children": [ { "kind": "representation", "params": { "type": "sphere" }, "children": [ { "kind": "color", "params": { "color": "purple" } } ] } ] } ] } ] } ] } ] } } }, { "id": "grd-ligand-3ptb-ca", "prompt": "Load 3PTB; show the protein as a grey cartoon and the CA as orange ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Invalid parameters for node of kind \"component\":", " Invalid value for parameter \"selector\":", " \"CA\" is not a valid value for literal type (\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\")", " Invalid value \"CA\" supplied to : ((\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\") | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>)/1: { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }", " Invalid value \"CA\" supplied to : ((\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\") | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>)/2: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/3ptb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "CA" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] } ] } ] } ] } ] } } }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 22 column 1 (char 1624)", "raw": "```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": [{\"auth_asym_id\": \"A\", \"auth_seq_id\": 57}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 102}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 195}]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]},\n {\"kind\": \"primitives\", \"params\": {\"color\": \"yellow\", \"label_color\": \"yellow\"}, \"children\": [\n {\"kind\": \"primitive\", \"params\": {\"kind\": \"distance_measurement\",\n \"start\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 57, \"label_atom_id\": \"NE2\"},\n \"end\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 195, \"label_atom_id\": \"OG\"},\n \"radius\": 0.06, \"dash_length\": 0.15, \"label_template\": \"{{distance}}\"}}]},\n {\"kind\": \"primitive\", \"params\": {\"kind\": \"distance_measurement\",\n \"start\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 102, \"label_atom_id\": \"OD1\"},\n \"end\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 195, \"label_atom_id\": \"OG\"},\n \"radius\": 0.06, \"dash_length\": 0.15, \"label_template\": \"{{distance}}\"}}]}\n ]}]}]}\n]}}\n```" }, { "id": "int-004", "prompt": "Load 1A6M with the protein as a grey cartoon and show all the non-covalent interactions (hydrogen bonds, metal contacts) around the bound oxygen molecule.", "outcome": "invalid_mvs", "mvs_issues": [ "Unknown node kind \"custom\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1a6m.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" } } ] }, { "kind": "component", "params": { "selector": "ligand", "auth_comp_id": "OXY" }, "children": [ { "kind": "custom", "params": { "molstar_show_non_covalent_interactions": true, "molstar_non_covalent_interactions_radius_ang": 5 } } ] } ] } ] } ] } ] } } }, { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "invalid_mvs", "mvs_issues": [ "Unknown node kind \"custom\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/3ptb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand", "model_index": 0 }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" } }, { "kind": "custom", "params": { "molstar_show_non_covalent_interactions": true, "molstar_non_covalent_interactions_radius_ang": 5 } } ] } ] } ] } ] } ] } } } ] }, "gpt-5.4-nano": { "outcomes": { "valid": 53, "unchecked": 0, "invalid_json": 15, "not_mvs": 0, "invalid_mvs": 2, "load_failed": 0 }, "n": 70, "mvs_f1": 0.6541, "failures": [ { "id": "mvs-001", "prompt": "Load haemoglobin (PDB 1HHO) and show the protein as a grey cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 457 (char 456)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1HHO.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]}]}]}]}]}}}" }, { "id": "mvs-003", "prompt": "Load hen egg-white lysozyme (1LYZ) as a grey cartoon, and show the two catalytic residues Glu35 and Asp52 on chain A as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 892 (char 891)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1LYZ.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":35}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":52}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}]}}" }, { "id": "clinvar-1tup-F109", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant F109V as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 535 (char 534)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":109}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"},\"custom\":{\"molstar_color_theme_name\":null}}]}]}]}]}]}]}}}" }, { "id": "clinvar-1tup-N239", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant N239T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 505 (char 504)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":239}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"},\"children\":[]}]}]}]}]}]}]}]}}" }, { "id": "clinvar-1tup-S215", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S215T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 504 (char 503)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":215}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"},\"custom\":{}}]}]}]}]}]}]}}}" }, { "id": "hotspots-1tup", "prompt": "In p53 (PDB 1TUP), chain A, highlight the 6 mutational hotspot residues — the positions carrying the most pathogenic ClinVar variants — as red spheres.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 1867 (char 1866)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1TUP.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":175}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\",\"size_factor\":1.0},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"},\"custom\":{\"molstar_theme\":\"single-color\"} }]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":248}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\",\"size_factor\":1.0},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"},\"custom\":{\"molstar_theme\":\"single-color\"} }]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":249}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\",\"size_factor\":1.0},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"},\"custom\":{\"molstar_theme\":\"single-color\"} }]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":273}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\",\"size_factor\":1.0},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"},\"custom\":{\"molstar_theme\":\"single-color\"} }]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":282}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\",\"size_factor\":1.0},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"},\"custom\":{\"molstar_theme\":\"single-color\"} }]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":286}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\",\"size_factor\":1.0},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"},\"custom\":{\"molstar_theme\":\"single-color\"} }]}]}]}]}]}]}}]}" }, { "id": "gen-cartoon-1hho", "prompt": "Load haemoglobin (1HHO) and show the protein as a red cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 440 (char 439)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}}}" }, { "id": "gen-chain-1lyz", "prompt": "Load 1LYZ; show everything as a grey cartoon, then colour chain A green.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"component\" cannot appear as a child of \"component\". Allowed parents for \"component\" are: \"structure\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1LYZ.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model", "model_index": 0 }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } }, { "kind": "opacity", "params": { "opacity": 1 } } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A" } }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "green" } } ] } ] } ] } ] } ] } ] } ] } } }, { "id": "gen-chain-2hhb", "prompt": "Load 2HHB; show everything as a grey cartoon, then colour chain B teal.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 660 (char 659)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"teal\"}}]}]}]}]}]}]}]}]}}}" }, { "id": "gen-chain-4ins", "prompt": "Load 4INS; show everything as a grey cartoon, then colour chain B blue.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 644 (char 643)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"blue\"}}]}]}]}]}]}]}}}" }, { "id": "gen-surface-1cbs", "prompt": "Load 1CBS; render the protein as a steelblue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 462 (char 461)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1CBS.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"steelblue\"}}]}]}]}]}]}]}}}" }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1240 (char 1239)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":64,\"label_comp_id\":\"HIS\"}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"label_comp_id\":\"O2\"}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":64,\"label_atom_id\":\"NE2\"},\"end\":{\"auth_asym_id\":\"A\",\"label_comp_id\":\"O2\",\"label_atom_id\":\"O2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}]}]}]}]}]}]}}" }, { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"component\" cannot appear as a child of \"component\". Allowed parents for \"component\" are: \"structure\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/3ptb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] }, { "kind": "component", "params": { "selector": { "label_comp_id": "BEN" } }, "custom": { "molstar_show_non_covalent_interactions": true, "molstar_non_covalent_interactions_radius_ang": 5 } } ] } ] } ] } ] } ] } } }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 1088 (char 1087)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/6MSM.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"C\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1.2},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"dodgerblue\"},\"custom\":{\"molstar_color_theme_name\":\"chain-id\"}}]}],\"custom\":{\"molstar_show_non_covalent_interactions\":false}},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"C\",\"beg_auth_seq_id\":1,\"end_auth_seq_id\":1480}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"backbone\",\"size_factor\":1.1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"dodgerblue\"}}]}],\"custom\":{\"molstar_show_non_covalent_interactions\":false}}]}]}]}]}}]}" }, { "id": "res-gfp", "prompt": "show green fluorescent protein from Aequorea victoria", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 468 (char 467)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2b3p.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"lime\"}}]}]}]}]}]}]}}}" }, { "id": "res-lysozyme", "prompt": "Show me hen egg white lysozyme", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 446 (char 445)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1LYZ.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"lightgray\"}}]}]}]}]}]}]}}}" }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 856 (char 855)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/5n74.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"slategray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":0.9},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ion\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\",\"size_factor\":0.6},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gold\"}}]}]}]}]}]}]}}]}" } ] }, "meta-llama/llama-4-maverick": { "outcomes": { "valid": 57, "unchecked": 0, "invalid_json": 1, "not_mvs": 0, "invalid_mvs": 11, "load_failed": 1 }, "n": 70, "mvs_f1": 0.792, "failures": [ { "id": "clinvar-1tup-D281", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant D281Y as red ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "lightgrey" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 281 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "focus", "params": { "radius": 10 }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 281 } } } ] } ] } ] } ] } ] } } }, { "id": "clinvar-1tup-F109", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant F109V as red ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "lightgrey" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 109 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 } } ] } ] } ] } ] } } }, { "id": "clinvar-1tup-N239", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant N239T as red ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "grey" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 239 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "focus", "params": {}, "children": [] } ] } ] } ] } ] } } }, { "id": "clinvar-1tup-S215", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S215T as red ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 215 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "focus", "params": { "radius": 10 } } ] } ] } ] } ] } } }, { "id": "hotspots-1tup", "prompt": "In p53 (PDB 1TUP), chain A, highlight the 6 mutational hotspot residues — the positions carrying the most pathogenic ClinVar variants — as red spheres.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": [ { "auth_asym_id": "A", "auth_seq_id": 175 }, { "auth_asym_id": "A", "auth_seq_id": 245 }, { "auth_asym_id": "A", "auth_seq_id": 248 }, { "auth_asym_id": "A", "auth_seq_id": 249 }, { "auth_asym_id": "A", "auth_seq_id": 273 }, { "auth_asym_id": "A", "auth_seq_id": 281 } ] }, "children": [ { "kind": "representation", "params": { "type": "spacefill" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "focus", "params": { "radius": 20 } } ] } ] } ] } ] } } }, { "id": "gen-surface-3ptb", "prompt": "Load 3PTB; render the protein as a plum molecular surface.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/3ptb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "surface" }, "children": [ { "kind": "color", "params": { "color": "plum" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "load_failed", "load_error": "render failed: Error: FormatError\n at j_ (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7670:159)\n at Cwt (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7677:56875)\n at e.f (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7677:56472)\n at HJ (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:35:61538)\n at tG (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:35:60775)\n at lF.run (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7586:109461)\n at r4.runTask (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7586:123836)\n at tf (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7677:56495)\n at lY (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7675:29405)\n at e.loadMvsData (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7713:39371)", "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/3ptb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "grey" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand", "custom": { "molstar_show_non_covalent_interactions": true, "molstar_non_covalent_interactions_radius_ang": 5 } } } ] } ] } ] } ] } } }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 58 column 2 (char 1532)", "raw": "```json\n{\n \"root\": {\n \"kind\": \"root\",\n \"children\": [\n {\n \"kind\": \"download\",\n \"params\": {\n \"url\": \"https://files.rcsb.org/download/5j3i.cif\"\n },\n \"children\": [\n {\n \"kind\": \"parse\",\n \"params\": {\n \"format\": \"mmcif\"\n },\n \"children\": [\n {\n \"kind\": \"structure\",\n \"params\": {\n \"type\": \"model\"\n },\n \"children\": [\n {\n \"kind\": \"component\",\n \"params\": {\n \"selector\": \"polymer\"\n },\n \"children\": [\n {\n \"kind\": \"representation\",\n \"params\": {\n \"type\": \"cartoon\"\n },\n \"children\": [\n {\n \"kind\": \"color\",\n \"params\": {\n \"color\": \"steelblue\"\n },\n \"custom\": {\n \"molstar_color_theme_name\": \"chain-id\"\n }\n }\n ]\n }\n ]\n },\n {\n \"kind\": \"focus\"\n }\n ]\n }\n ]\n }\n ]\n }\n ]\n}\n```" }, { "id": "res-gfp", "prompt": "show green fluorescent protein from Aequorea victoria", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1hgp.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "green" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "res-lysozyme", "prompt": "Show me hen egg white lysozyme", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1eze.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "res-myoglobin", "prompt": "Show me sperm whale myoglobin", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1wnm.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/4k1u.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "res-pde5a", "prompt": "I wanna see a structure of PDE5A", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1TUP.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } } ] }, "minimax/minimax-m3": { "outcomes": { "valid": 63, "unchecked": 0, "invalid_json": 5, "not_mvs": 0, "invalid_mvs": 2, "load_failed": 0 }, "n": 70, "mvs_f1": 0.8166, "failures": [ { "id": "mvs-004", "prompt": "Load HIV-1 protease (1HVR); protein as grey cartoon, the bound inhibitor as magenta ball-and-stick, and focus the camera on the inhibitor.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 588 (char 587)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hvr.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\":" }, { "id": "hotspots-1tup", "prompt": "In p53 (PDB 1TUP), chain A, highlight the 6 mutational hotspot residues — the positions carrying the most pathogenic ClinVar variants — as red spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 22 column 1 (char 883)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": [\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 175},\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 245},\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 248},\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 249},\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 273},\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 282}\n ]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"spacefill\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}},\n {\"kind\": \"focus\"}\n ]}\n ]}\n ]}]}\n ]}\n ]}\n]}" }, { "id": "gen-ions-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 745)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": \"ion\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"spacefill\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"purple\"}}]}]}\n ]}]}\n ]}]}\n]}" }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 31 column 1 (char 1807)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": [\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 57},\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 102},\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 195}\n ]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"#FFFFFF\"},\n \"custom\": {\"molstar_color_theme_name\": \"element-symbol\"}}]}]},\n {\"kind\": \"primitives\", \"params\": {\"color\": \"yellow\", \"label_color\": \"yellow\"}, \"children\": [\n {\"kind\": \"primitive\", \"params\": {\"kind\": \"distance_measurement\",\n \"start\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 57, \"label_atom_id\": \"NE2\"},\n \"end\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 195, \"label_atom_id\": \"OG\"},\n \"color\": \"yellow\", \"radius\": 0.06, \"dash_length\": 0.15,\n \"label_template\": \"{{distance}}\"}},\n {\"kind\": \"primitive\", \"params\": {\"kind\": \"distance_measurement\",\n \"start\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 102, \"label_atom_id\": \"OD1\"},\n \"end\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 57, \"label_atom_id\": \"ND1\"},\n \"color\": \"yellow\", \"radius\": 0.06, \"dash_length\": 0.15,\n \"label_template\": \"{{distance}}\"}}\n ]}\n ]}]}\n ]}]}\n]}}" }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"representation\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/5uak.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } }, { "kind": "focus", "params": { "radius": 120, "radius_extra": 30 } } ] } ] } ] } ] } ] } ] } } }, { "id": "res-lysozyme", "prompt": "Show me hen egg white lysozyme", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1aki.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "white" }, "custom": { "molstar_color_theme_name": "sequence-id" } } ] } ] }, { "kind": "focus", "params": { "radius": 25 } } ] } ] } ] } ] } } } ] }, "moonshotai/kimi-k2.6": { "outcomes": { "valid": 51, "unchecked": 0, "invalid_json": 18, "not_mvs": 0, "invalid_mvs": 1, "load_failed": 0 }, "n": 70, "mvs_f1": 0.6569, "failures": [ { "id": "mvs-004", "prompt": "Load HIV-1 protease (1HVR); protein as grey cartoon, the bound inhibitor as magenta ball-and-stick, and focus the camera on the inhibitor.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "clinvar-1tup-D281", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant D281Y as red ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "named-1tup-143", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 143 and show it as blue ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 143 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "blue" } } ] } ] }, { "kind": "focus", "params": {} } ] } ] } ] } ] } } }, { "id": "gen-chain-1hho", "prompt": "Load 1HHO; show everything as a grey cartoon, then colour chain A red.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "gen-chain-4ins", "prompt": "Load 4INS; show everything as a grey cartoon, then colour chain B blue.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 12 column 5 (char 750)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/4ins.cif\"}, \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"all\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"grey\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"blue\"}}]}]}\n ]}]}\n ]}}\n]}}" }, { "id": "gen-focus-3ptb", "prompt": "Load 3PTB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 636 (char 635)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\",\"params\":{}}]}]}]}]}}" }, { "id": "gen-ligands-2hhb", "prompt": "Load 2HHB; show the protein as a grey cartoon and the ligands as teal ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 604 (char 603)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"teal\"}}]}]}]}]}]}}" }, { "id": "gen-range-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show residues 30-90 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 16 column 8 (char 833)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}\n ]}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"beg_auth_seq_id\": 30, \"end_auth_seq_id\": 90}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}\n ]}\n ]}\n ]}}\n ]}\n]}}" }, { "id": "gen-range-2hhb", "prompt": "Load 2HHB; protein as grey cartoon, and show residues 10-70 of chain B as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 720 (char 719)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/2hhb.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\", \"beg_auth_seq_id\": 10, \"end_auth_seq_id\": 70}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}}]}}" }, { "id": "gen-range-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show residues 50-110 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 721 (char 720)", "raw": " {\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"beg_auth_seq_id\": 50, \"end_auth_seq_id\": 110}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}}]}}" }, { "id": "gen-range-4ins", "prompt": "Load 4INS; protein as grey cartoon, and show residues 5-25 of chain B as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 16 column 8 (char 832)", "raw": " {\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/4ins.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}\n ]}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\", \"beg_auth_seq_id\": 5, \"end_auth_seq_id\": 25}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}\n ]}\n ]}\n ]}}\n ]}\n]}}" }, { "id": "grd-disulfide-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "grd-disulfide-4ins", "prompt": "Load 4INS; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "grd-ligand-3ptb-ca", "prompt": "Load 3PTB; show the protein as a grey cartoon and the CA as orange ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "int-002", "prompt": "Load 1A6M with the protein as a grey cartoon. Show the heme and the proximal histidine as ball-and-stick and measure the distance from the heme iron to the histidine's coordinating nitrogen.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "res-pde5a", "prompt": "I wanna see a structure of PDE5A", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" } ] }, "nvidia/nemotron-3-super-120b-a12b": { "outcomes": { "valid": 6, "unchecked": 0, "invalid_json": 64, "not_mvs": 0, "invalid_mvs": 0, "load_failed": 0 }, "n": 70, "mvs_f1": 0.078, "failures": [ { "id": "mvs-001", "prompt": "Load haemoglobin (PDB 1HHO) and show the protein as a grey cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 462 (char 461)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}]}]}]}]}]}" }, { "id": "mvs-002", "prompt": "Load haemoglobin (1HHO); show the protein as a grey cartoon and the heme groups as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 663 (char 662)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}]}]}" }, { "id": "mvs-003", "prompt": "Load hen egg-white lysozyme (1LYZ) as a grey cartoon, and show the two catalytic residues Glu35 and Asp52 on chain A as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 844 (char 843)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":35}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":52}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}]}}" }, { "id": "mvs-004", "prompt": "Load HIV-1 protease (1HVR); protein as grey cartoon, the bound inhibitor as magenta ball-and-stick, and focus the camera on the inhibitor.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 638 (char 637)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hvr.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\",\"params\":{}}]}]}]}]}]}]}" }, { "id": "mvs-005", "prompt": "Load insulin (4INS) and render the protein as a steel-blue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 467 (char 466)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/4ins.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"surface\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"steelblue\"}}]}]}]}]}]}]}]}" }, { "id": "clinvar-1tup-D281", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant D281Y as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 459 (char 458)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":281}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}]}" }, { "id": "clinvar-1tup-F109", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant F109V as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 459 (char 458)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":109}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}]}" }, { "id": "clinvar-1tup-N239", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant N239T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 636 (char 635)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":239}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}]}\"}" }, { "id": "clinvar-1tup-S215", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S215T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 460 (char 459)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":215}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}]}}" }, { "id": "clinvar-1tup-S241", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S241Y as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 500 (char 499)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 241}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}]}]}}" }, { "id": "named-1tup-143", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 143 and show it as blue ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 501 (char 500)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 143}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"blue\"}}]}]}]}]}]}]}]}" }, { "id": "named-1tup-175", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 175 and show it as blue ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 501 (char 500)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 175}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"blue\"}}]}]}]}]}]}]}]}" }, { "id": "named-1tup-248", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 248 and show it as blue ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 460 (char 459)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":248}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"blue\"}}]}]}]}]}]}]}]}" }, { "id": "gen-cartoon-1cbs", "prompt": "Load cellular retinoic-acid binding protein (1CBS) and show the protein as a purple cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 426 (char 425)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}]}]}" }, { "id": "gen-cartoon-1hho", "prompt": "Load haemoglobin (1HHO) and show the protein as a red cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 461 (char 460)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}]}\"}" }, { "id": "gen-cartoon-1lyz", "prompt": "Load lysozyme (1LYZ) and show the protein as a green cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 463 (char 462)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1lyz.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"green\"}}]}]}]}]}]}]}]}" }, { "id": "gen-cartoon-2hhb", "prompt": "Load deoxyhaemoglobin (2HHB) and show the protein as a teal cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 424 (char 423)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"teal\"}}]}]}]}]}]}]}]}" }, { "id": "gen-cartoon-3ptb", "prompt": "Load trypsin (3PTB) and show the protein as a orange cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 464 (char 463)", "raw": "\n\n{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}]}]}" }, { "id": "gen-cartoon-4ins", "prompt": "Load insulin (4INS) and show the protein as a blue cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 424 (char 423)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"blue\"}}]}]}]}]}]}]}]}" }, { "id": "gen-chain-1cbs", "prompt": "Load 1CBS; show everything as a grey cartoon, then colour chain A purple.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 497 (char 496)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"all\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}},{\"kind\":\"color\",\"params\":{\"color\":\"purple\"},\"selector\":{\"auth_asym_id\":\"A\"}}]}]}]}]}]}]}]}]}}" }, { "id": "gen-chain-1hho", "prompt": "Load 1HHO; show everything as a grey cartoon, then colour chain A red.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 611 (char 610)", "raw": "\n\n{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}]}]}" }, { "id": "gen-chain-1lyz", "prompt": "Load 1LYZ; show everything as a grey cartoon, then colour chain A green.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 608 (char 607)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"all\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"green\"}}]}]}]}]}]}]}]}}" }, { "id": "gen-chain-3ptb", "prompt": "Load 3PTB; show everything as a grey cartoon, then colour chain A orange.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 614 (char 613)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}\"}" }, { "id": "gen-chain-4ins", "prompt": "Load 4INS; show everything as a grey cartoon, then colour chain B blue.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 612 (char 611)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\"}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"blue\"}}]}]}]}]}]}]}]}" }, { "id": "gen-focus-1cbs", "prompt": "Load 1CBS; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 638 (char 637)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\",\"params\":{}}]}]}]}]}]}]}]}" }, { "id": "gen-focus-1hho", "prompt": "Load 1HHO; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 638 (char 637)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\",\"params\":{}}]}]}]}]}]}]}" }, { "id": "gen-focus-2hhb", "prompt": "Load 2HHB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 648 (char 647)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\",\"params\":{\"radius\":5}}]}]}]}]}]}]}]}}" }, { "id": "gen-focus-3ptb", "prompt": "Load 3PTB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 638 (char 637)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\",\"params\":{}}]}]}]}]}]}]}]}]}}" }, { "id": "gen-ions-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 600 (char 599)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ion\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}]}]}]}}" }, { "id": "gen-ions-2hhb", "prompt": "Load 2HHB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 600 (char 599)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ion\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}]}]}" }, { "id": "gen-ions-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 600 (char 599)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ion\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}]}]}" }, { "id": "gen-ligands-1cbs", "prompt": "Load 1CBS; show the protein as a grey cartoon and the ligands as purple ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 608 (char 607)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}]}]}]}" }, { "id": "gen-ligands-1hho", "prompt": "Load 1HHO; show the protein as a grey cartoon and the ligands as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 660 (char 659)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"grey\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}]}" }, { "id": "gen-ligands-2hhb", "prompt": "Load 2HHB; show the protein as a grey cartoon and the ligands as teal ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 606 (char 605)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"teal\"}}]}]}]}]}]}]}]}" }, { "id": "gen-ligands-3ptb", "prompt": "Load 3PTB; show the protein as a grey cartoon and the ligands as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 663 (char 662)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}]}]}]}" }, { "id": "gen-range-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show residues 30-90 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 722 (char 721)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"beg_auth_seq_id\": 30, \"end_auth_seq_id\": 90}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}]}]}}" }, { "id": "gen-range-1lyz", "prompt": "Load 1LYZ; protein as grey cartoon, and show residues 40-80 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 662 (char 661)", "raw": "\n\n{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":40,\"end_auth_seq_id\":80}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}]}}" }, { "id": "gen-range-2hhb", "prompt": "Load 2HHB; protein as grey cartoon, and show residues 10-70 of chain B as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 662 (char 661)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\",\"beg_auth_seq_id\":10,\"end_auth_seq_id\":70}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}]}\"}" }, { "id": "gen-range-4ins", "prompt": "Load 4INS; protein as grey cartoon, and show residues 5-25 of chain B as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 662 (char 661)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\",\"beg_auth_seq_id\":5,\"end_auth_seq_id\":25}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}\"}]}]}}" }, { "id": "gen-surface-1cbs", "prompt": "Load 1CBS; render the protein as a steelblue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 429 (char 428)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"steelblue\"}}]}]}]}]}]}]}]}" }, { "id": "gen-surface-1hho", "prompt": "Load 1HHO; render the protein as a steelblue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 429 (char 428)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"steelblue\"}}]}]}]}]}]}]}]}}" }, { "id": "gen-surface-1lyz", "prompt": "Load 1LYZ; render the protein as a khaki molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 463 (char 462)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1lyz.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"surface\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"khaki\"}}]}]}]}]}]}]}]}" }, { "id": "gen-surface-2hhb", "prompt": "Load 2HHB; render the protein as a salmon molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 426 (char 425)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"salmon\"}}]}]}]}]}]}]}]}]}" }, { "id": "gen-surface-3ptb", "prompt": "Load 3PTB; render the protein as a plum molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 424 (char 423)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"plum\"}}]}]}]}]}]}]}]}]}}" }, { "id": "gen-surface-4ins", "prompt": "Load 4INS; render the protein as a salmon molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 426 (char 425)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"salmon\"}}]}]}]}]}]}]}]}" }, { "id": "grd-disulfide-1lyz", "prompt": "Load 1LYZ; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1074 (char 1073)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"CYS\",\"auth_seq_id\":6},{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"CYS\",\"auth_seq_id\":127},{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"CYS\",\"auth_seq_id\":30},{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"CYS\",\"auth_seq_id\":115},{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"CYS\",\"auth_seq_id\":64},{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"CYS\",\"auth_seq_id\":80},{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"CYS\",\"auth_seq_id\":76},{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"CYS\",\"auth_seq_id\":94}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"yellow\"}}]}]}]}]}]}]}]}" }, { "id": "grd-disulfide-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 701 (char 700)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": {\"label_asym_id\": \"A\", \"label_comp_id\": \"CYS\"}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"yellow\"}}]}]}]}]}]}]}]}" }, { "id": "grd-ligand-1cbs-rea", "prompt": "Load 1CBS; show the protein as a grey cartoon and the REA as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 623 (char 622)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"REA\"}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}" }, { "id": "grd-ligand-1hho-hem", "prompt": "Load 1HHO; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 623 (char 622)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"HEM\"}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}" }, { "id": "grd-ligand-2hhb-hem", "prompt": "Load 2HHB; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 623 (char 622)", "raw": "\n\n{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"HEM\"}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}]}" }, { "id": "grd-ligand-3ptb-ca", "prompt": "Load 3PTB; show the protein as a grey cartoon and the CA as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 622 (char 621)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"label_atom_id\":\"CA\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}]}}" }, { "id": "grd-ligand-4ins-zn", "prompt": "Load 4INS; show the protein as a grey cartoon and the ZN as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 622 (char 621)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"ZN\"}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}]}]}}" }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1050 (char 1049)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":64}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"}}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"OXY\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"}}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":64,\"label_atom_id\":\"NE2\"},\"end\":{\"auth_comp_id\":\"OXY\",\"label_atom_id\":\"O2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}]}]}]}]}]}]}" }, { "id": "int-002", "prompt": "Load 1A6M with the protein as a grey cartoon. Show the heme and the proximal histidine as ball-and-stick and measure the distance from the heme iron to the histidine's coordinating nitrogen.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1067 (char 1066)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"HEM\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"}}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":93}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"}}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"HEM\",\"auth_atom_id\":\"FE\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":93,\"auth_atom_id\":\"NE2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}]}]}]}]}]}]}\"}" }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1268 (char 1267)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":57},{\"auth_asym_id\":\"A\",\"auth_seq_id\":102},{\"auth_asym_id\":\"A\",\"auth_seq_id\":195}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"}}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":57,\"label_atom_id\":\"ND1\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":102,\"label_atom_id\":\"OD2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}},{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":57,\"label_atom_id\":\"NE2\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":195,\"label_atom_id\":\"OG\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}]}]}]}]}]}]}]}}" }, { "id": "int-004", "prompt": "Load 1A6M with the protein as a grey cartoon and show all the non-covalent interactions (hydrogen bonds, metal contacts) around the bound oxygen molecule.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 616 (char 615)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"label_comp_id\":\"OXY\"}},\"custom\":{\"molstar_show_non_covalent_interactions\":true,\"molstar_non_covalent_interactions_radius_ang\":5}}]}]}]}]}]}]}}" }, { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 728 (char 727)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\",\"custom\":{\"molstar_show_non_covalent_interactions\":true,\"molstar_non_covalent_interactions_radius_ang\":5}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"BZN\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}" }, { "id": "int-006", "prompt": "Load haemoglobin 1HHO; show the protein as a 50% transparent surface and the heme groups as ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 667 (char 666)", "raw": "\n\n{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}},{\"kind\":\"opacity\",\"params\":{\"opacity\":0.5}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"HEM\"}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}" }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 462 (char 461)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/6djz.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}]}]}]}]}]}" }, { "id": "res-gfp", "prompt": "show green fluorescent protein from Aequorea victoria", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 463 (char 462)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1ema.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"green\"}}]}]}]}]}]}]}]}" }, { "id": "res-lysozyme", "prompt": "Show me hen egg white lysozyme", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 462 (char 461)", "raw": "\n\n{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hel.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}]}]}]}]}]}" }, { "id": "res-myoglobin", "prompt": "Show me sperm whale myoglobin", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 467 (char 466)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1mbn.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"slategray\"}}]}]}]}]}]}]}]}" }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 424 (char 423)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2p16.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]}]}]}]}]}]}}" }, { "id": "res-pde5a", "prompt": "I wanna see a structure of PDE5A", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 424 (char 423)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1udt.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]}]}]}]}]}]}" } ] }, "openai/gpt-oss-120b": { "outcomes": { "valid": 44, "unchecked": 0, "invalid_json": 26, "not_mvs": 0, "invalid_mvs": 0, "load_failed": 0 }, "n": 70, "mvs_f1": 0.5614, "failures": [ { "id": "mvs-004", "prompt": "Load HIV-1 protease (1HVR); protein as grey cartoon, the bound inhibitor as magenta ball-and-stick, and focus the camera on the inhibitor.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 632 (char 631)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hvr.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\",\"params\":{}}]}]}}]}]}}" }, { "id": "mvs-005", "prompt": "Load insulin (4INS) and render the protein as a steel-blue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 468 (char 467)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/4INS.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"surface\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"steelblue\"}}]}]}]}]}]}]}}}" }, { "id": "clinvar-1tup-D281", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant D281Y as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 474 (char 473)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":281}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]},{\"kind\":\"focus\"}]}]}]}]}}]}}" }, { "id": "clinvar-1tup-F109", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant F109V as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 663 (char 662)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"lightgray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":109}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]},{\"kind\":\"focus\",\"params\":{}}]}]}}]}]}}" }, { "id": "clinvar-1tup-S241", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S241Y as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 498 (char 497)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 241}},\"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"},\"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}]}}" }, { "id": "hotspots-1tup", "prompt": "In p53 (PDB 1TUP), chain A, highlight the 6 mutational hotspot residues — the positions carrying the most pathogenic ClinVar variants — as red spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 645 (char 644)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":175},{\"auth_asym_id\":\"A\",\"auth_seq_id\":245},{\"auth_asym_id\":\"A\",\"auth_seq_id\":248},{\"auth_asym_id\":\"A\",\"auth_seq_id\":249},{\"auth_asym_id\":\"A\",\"auth_seq_id\":273},{\"auth_asym_id\":\"A\",\"auth_seq_id\":282}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}}]}]}}" }, { "id": "named-1tup-248", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 248 and show it as blue ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 458 (char 457)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":248}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"blue\"}}]}]}]}]}]}}]}}" }, { "id": "gen-cartoon-1cbs", "prompt": "Load cellular retinoic-acid binding protein (1CBS) and show the protein as a purple cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 424 (char 423)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}}]}}" }, { "id": "gen-cartoon-1hho", "prompt": "Load haemoglobin (1HHO) and show the protein as a red cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 461 (char 460)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}]}}" }, { "id": "gen-cartoon-3ptb", "prompt": "Load trypsin (3PTB) and show the protein as a orange cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 424 (char 423)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3PTB.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}]}}" }, { "id": "gen-cartoon-4ins", "prompt": "Load insulin (4INS) and show the protein as a blue cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 422 (char 421)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"blue\"}}]}]}]}]}]}}]}}" }, { "id": "gen-focus-1hho", "prompt": "Load 1HHO; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 620 (char 619)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\"}]}]}}]}]}}" }, { "id": "gen-focus-2hhb", "prompt": "Load 2HHB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 624 (char 623)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\"}]}]}]}]}}]}}" }, { "id": "gen-ions-4ins", "prompt": "Load 4INS; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 598 (char 597)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ion\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}}]}}" }, { "id": "gen-range-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show residues 50-110 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 657 (char 656)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":50,\"end_auth_seq_id\":110}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}}]}]}}}" }, { "id": "gen-surface-1hho", "prompt": "Load 1HHO; render the protein as a steelblue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 427 (char 426)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"steelblue\"}}]}]}]}]}]}}]}}" }, { "id": "gen-surface-1lyz", "prompt": "Load 1LYZ; render the protein as a khaki molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 423 (char 422)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"khaki\"}}]}]}]}]}]}}]}}" }, { "id": "gen-surface-2hhb", "prompt": "Load 2HHB; render the protein as a salmon molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 422 (char 421)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"salmon\"}}]}]}]}]}}]}}" }, { "id": "grd-ligand-4ins-zn", "prompt": "Load 4INS; show the protein as a grey cartoon and the ZN as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 595 (char 594)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ion\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}}]}]}]}]}}" }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1025 (char 1024)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":64},{\"auth_asym_id\":\"A\",\"label_comp_id\":\"O2\"}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":64,\"label_atom_id\":\"NE2\"},\"end\":{\"auth_asym_id\":\"A\",\"label_comp_id\":\"O2\",\"label_atom_id\":\"O2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}]}]}}]}]}}}" }, { "id": "int-002", "prompt": "Load 1A6M with the protein as a grey cartoon. Show the heme and the proximal histidine as ball-and-stick and measure the distance from the heme iron to the histidine's coordinating nitrogen.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1166 (char 1165)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":93}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"label_comp_id\":\"HEM\",\"label_atom_id\":\"FE\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":93,\"label_atom_id\":\"NE2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}]}]}}]}}]}}" }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1055 (char 1054)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":57},{\"auth_asym_id\":\"A\",\"auth_seq_id\":102},{\"auth_asym_id\":\"A\",\"auth_seq_id\":195}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":57,\"label_atom_id\":\"ND1\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":102,\"label_atom_id\":\"OD1\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}},{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":57,\"label_atom_id\":\"NE2\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":195,\"label_atom_id\":\"OG\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}}]}}]}}]}}" }, { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 708 (char 707)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"custom\":{\"molstar_show_non_covalent_interactions\":true,\"molstar_non_covalent_interactions_radius_ang\":5},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}}]}}]}}" }, { "id": "res-gfp", "prompt": "show green fluorescent protein from Aequorea victoria", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 440 (char 439)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1ema.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"green\"}},{\"kind\":\"focus\"}]}]}]}]}]}}]}}" }, { "id": "res-lysozyme", "prompt": "Show me hen egg white lysozyme", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 463 (char 462)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1aki.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\",\"custom\":{\"molstar_color_theme_name\":\"chain-id\"}}}]}},{\"kind\":\"label\",\"params\":{\"text\":\"Hen Egg White Lysozyme\"}},{\"kind\":\"focus\"}]}]}]}}]}}" }, { "id": "res-myoglobin", "prompt": "Show me sperm whale myoglobin", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 444 (char 443)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1M6C.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"lightgray\"}}]},{\"kind\":\"focus\"}]}]}]}]}}]}}" } ] }, "openai/gpt-oss-20b": { "outcomes": { "valid": 20, "unchecked": 0, "invalid_json": 50, "not_mvs": 0, "invalid_mvs": 0, "load_failed": 0 }, "n": 70, "mvs_f1": 0.2524, "failures": [ { "id": "mvs-001", "prompt": "Load haemoglobin (PDB 1HHO) and show the protein as a grey cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 422 (char 421)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]}]}]}]}}" }, { "id": "mvs-003", "prompt": "Load hen egg-white lysozyme (1LYZ) as a grey cartoon, and show the two catalytic residues Glu35 and Asp52 on chain A as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 668 (char 667)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":35},{\"auth_asym_id\":\"A\",\"auth_seq_id\":52}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}}]}]}}" }, { "id": "mvs-004", "prompt": "Load HIV-1 protease (1HVR); protein as grey cartoon, the bound inhibitor as magenta ball-and-stick, and focus the camera on the inhibitor.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 624 (char 623)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hvr.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\"}]}]}]}]}}" }, { "id": "clinvar-1tup-F109", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant F109V as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 633 (char 632)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":109}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}}" }, { "id": "clinvar-1tup-N239", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant N239T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 633 (char 632)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":239}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}}" }, { "id": "clinvar-1tup-S215", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S215T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 711 (char 710)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":215}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]},{\"kind\":\"focus\",\"params\":{\"radius\":5}}]}]}}]}]}}" }, { "id": "clinvar-1tup-S241", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S241Y as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 681 (char 680)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"}, \"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1.0},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":241}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]},{\"kind\":\"focus\",\"params\":{}}]}]}]}]}}" }, { "id": "hotspots-1tup", "prompt": "In p53 (PDB 1TUP), chain A, highlight the 6 mutational hotspot residues — the positions carrying the most pathogenic ClinVar variants — as red spheres.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "named-1tup-143", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 143 and show it as blue ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 458 (char 457)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":143}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"blue\"}}]}]}]}]}]}}" }, { "id": "gen-cartoon-1lyz", "prompt": "Load lysozyme (1LYZ) and show the protein as a green cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 423 (char 422)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"green\"}}]}]}]}]}]}}" }, { "id": "gen-chain-1hho", "prompt": "Load 1HHO; show everything as a grey cartoon, then colour chain A red.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 604 (char 603)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}}]}]}}" }, { "id": "gen-chain-1lyz", "prompt": "Load 1LYZ; show everything as a grey cartoon, then colour chain A green.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 610 (char 609)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"green\"}}]}]}]}]}]}}" }, { "id": "gen-chain-2hhb", "prompt": "Load 2HHB; show everything as a grey cartoon, then colour chain B teal.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 609 (char 608)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"teal\"}}]}]}]}]}]}}" }, { "id": "gen-chain-3ptb", "prompt": "Load 3PTB; show everything as a grey cartoon, then colour chain A orange.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 611 (char 610)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-chain-4ins", "prompt": "Load 4INS; show everything as a grey cartoon, then colour chain B blue.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 609 (char 608)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"blue\"}}]}]}]}]}]}}" }, { "id": "gen-focus-1cbs", "prompt": "Load 1CBS; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 647 (char 646)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\",\"params\":{\"radius\":10}}]}]}]}]}}" }, { "id": "gen-focus-1hho", "prompt": "Load 1HHO; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 672 (char 671)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\"}]}]}]}]}}" }, { "id": "gen-focus-2hhb", "prompt": "Load 2HHB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 654 (char 653)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\",\"params\":{}}]}]}]}]}]}" }, { "id": "gen-focus-3ptb", "prompt": "Load 3PTB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 624 (char 623)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\"}]}]}]}]}}" }, { "id": "gen-ions-2hhb", "prompt": "Load 2HHB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 598 (char 597)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ion\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}}" }, { "id": "gen-ions-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 598 (char 597)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ion\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}}" }, { "id": "gen-ions-4ins", "prompt": "Load 4INS; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 598 (char 597)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ion\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}}" }, { "id": "gen-ligands-1cbs", "prompt": "Load 1CBS; show the protein as a grey cartoon and the ligands as purple ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 606 (char 605)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1CBS.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}}" }, { "id": "gen-ligands-1hho", "prompt": "Load 1HHO; show the protein as a grey cartoon and the ligands as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 603 (char 602)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}}" }, { "id": "gen-ligands-3ptb", "prompt": "Load 3PTB; show the protein as a grey cartoon and the ligands as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 606 (char 605)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-range-1cbs", "prompt": "Load 1CBS; protein as grey cartoon, and show residues 20-60 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 660 (char 659)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1CBS.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":20,\"end_auth_seq_id\":60}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-range-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show residues 30-90 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 660 (char 659)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":30,\"end_auth_seq_id\":90}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-range-1lyz", "prompt": "Load 1LYZ; protein as grey cartoon, and show residues 40-80 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 660 (char 659)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":40,\"end_auth_seq_id\":80}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-range-2hhb", "prompt": "Load 2HHB; protein as grey cartoon, and show residues 10-70 of chain B as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 660 (char 659)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\",\"beg_auth_seq_id\":10,\"end_auth_seq_id\":70}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-range-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show residues 50-110 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 661 (char 660)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":50,\"end_auth_seq_id\":110}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-surface-1cbs", "prompt": "Load 1CBS; render the protein as a steelblue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 427 (char 426)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"steelblue\"}}]}]}]}]}]}}" }, { "id": "gen-surface-1lyz", "prompt": "Load 1LYZ; render the protein as a khaki molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 423 (char 422)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"khaki\"}}]}]}]}]}]}}" }, { "id": "gen-surface-2hhb", "prompt": "Load 2HHB; render the protein as a salmon molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 424 (char 423)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"salmon\"}}]}]}]}]}]}}" }, { "id": "gen-surface-4ins", "prompt": "Load 4INS; render the protein as a salmon molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 424 (char 423)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"salmon\"}}]}]}]}]}]}}" }, { "id": "grd-disulfide-1lyz", "prompt": "Load 1LYZ; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 655 (char 654)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"CYS\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"yellow\"}}]}]}]}]}]}}" }, { "id": "grd-disulfide-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 618 (char 617)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"label_comp_id\":\"CYS\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"yellow\"}}]}]}]}]]}}" }, { "id": "grd-disulfide-4ins", "prompt": "Load 4INS; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1485 (char 1484)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":7}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"yellow\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":11}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"yellow\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":20}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"yellow\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\",\"auth_seq_id\":7}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"yellow\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\",\"auth_seq_id\":19}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"yellow\"}}]}]}]}]}]}}" }, { "id": "grd-ligand-1cbs-rea", "prompt": "Load 1CBS; show the protein as a grey cartoon and the REA as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 619 (char 618)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"REA\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]]}}" }, { "id": "grd-ligand-1hho-hem", "prompt": "Load 1HHO; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 608 (char 607)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}" }, { "id": "grd-ligand-2hhb-hem", "prompt": "Load 2HHB; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 622 (char 621)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"HEM\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}" }, { "id": "grd-ligand-3ptb-ca", "prompt": "Load 3PTB; show the protein as a grey cartoon and the CA as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 619 (char 618)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_atom_id\":\"CA\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "grd-ligand-4ins-zn", "prompt": "Load 4INS; show the protein as a grey cartoon and the ZN as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 619 (char 618)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"ZN\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1035 (char 1034)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":64}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"}}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"}}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":64,\"label_atom_id\":\"NE2\"},\"end\":{\"label_comp_id\":\"OXY\",\"label_atom_id\":\"O2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}]}]}]}]}}" }, { "id": "int-002", "prompt": "Load 1A6M with the protein as a grey cartoon. Show the heme and the proximal histidine as ball-and-stick and measure the distance from the heme iron to the histidine's coordinating nitrogen.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "int-004", "prompt": "Load 1A6M with the protein as a grey cartoon and show all the non-covalent interactions (hydrogen bonds, metal contacts) around the bound oxygen molecule.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 744 (char 743)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\",\"custom\":{\"molstar_show_non_covalent_interactions\":true,\"molstar_non_covalent_interactions_radius_ang\":5}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 648 (char 647)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\"},{\"auth_comp_id\":\"BZD\"}]},\"children\":[{\"kind\":\"custom\",\"params\":{\"molstar_show_non_covalent_interactions\":true,\"molstar_non_covalent_interactions_radius_ang\":5}}]}]}]}]}}" }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 422 (char 421)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/6MSM.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]}]}]}]}}" }, { "id": "res-myoglobin", "prompt": "Show me sperm whale myoglobin", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 606 (char 605)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 422 (char 421)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4k7a.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]}]}]}]}}" } ] }, "qwen/qwen3-30b-a3b-instruct-2507": { "outcomes": { "valid": 39, "unchecked": 0, "invalid_json": 28, "not_mvs": 0, "invalid_mvs": 3, "load_failed": 0 }, "n": 70, "mvs_f1": 0.5194, "raw_missing": true, "failures": [ { "id": "mvs-004", "prompt": "Load HIV-1 protease (1HVR); protein as grey cartoon, the bound inhibitor as magenta ball-and-stick, and focus the camera on the inhibitor.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1hvr.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "label_comp_id": "M25", "auth_seq_id": 1 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 1.5 }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "label_comp_id": "M25", "auth_seq_id": 1 } } } ] } ] } ] } ] } ] } } }, { "id": "clinvar-1tup-D281", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant D281Y as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 8 column 69 (char 546)", "raw": null }, { "id": "clinvar-1tup-F109", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant F109V as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 8 column 69 (char 546)", "raw": null }, { "id": "clinvar-1tup-S215", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S215T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 10 column 1 (char 553)", "raw": null }, { "id": "hotspots-1tup", "prompt": "In p53 (PDB 1TUP), chain A, highlight the 6 mutational hotspot residues — the positions carrying the most pathogenic ClinVar variants — as red spheres.", "outcome": "invalid_mvs", "mvs_issues": [ "Invalid parameters for node of kind \"component\":", " Invalid value for parameter \"selector\":", " \"[object Object]\" is not a valid value for literal type (\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\")", " Invalid value [135,143,155,175,245,248] supplied to : ((\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\") | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>)/1: { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }/auth_seq_id: Integer", " Invalid value {\"auth_asym_id\":\"A\",\"auth_seq_id\":[135,143,155,175,245,248]} supplied to : ((\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\") | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>)/2: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": [ 135, 143, 155, 175, 245, 248 ] } }, "children": [ { "kind": "representation", "params": { "type": "spacefill", "size_factor": 1.0 }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] } ] } ] } ] } ] } } }, { "id": "named-1tup-143", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 143 and show it as blue ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 11 column 14 (char 571)", "raw": null }, { "id": "named-1tup-248", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 248 and show it as blue ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 8 column 70 (char 547)", "raw": null }, { "id": "gen-chain-1cbs", "prompt": "Load 1CBS; show everything as a grey cartoon, then colour chain A purple.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 747)", "raw": null }, { "id": "gen-chain-3ptb", "prompt": "Load 3PTB; show everything as a grey cartoon, then colour chain A orange.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 747)", "raw": null }, { "id": "gen-focus-1cbs", "prompt": "Load 1CBS; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 14 column 14 (char 879)", "raw": null }, { "id": "gen-ions-4ins", "prompt": "Load 4INS; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 737)", "raw": null }, { "id": "gen-range-1cbs", "prompt": "Load 1CBS; protein as grey cartoon, and show residues 20-60 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 806)", "raw": null }, { "id": "gen-range-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show residues 50-110 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 807)", "raw": null }, { "id": "gen-range-4ins", "prompt": "Load 4INS; protein as grey cartoon, and show residues 5-25 of chain B as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 805)", "raw": null }, { "id": "gen-surface-1hho", "prompt": "Load 1HHO; render the protein as a steelblue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 11 column 14 (char 537)", "raw": null }, { "id": "gen-surface-4ins", "prompt": "Load 4INS; render the protein as a salmon molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 12 column 1 (char 535)", "raw": null }, { "id": "grd-disulfide-1lyz", "prompt": "Load 1LYZ; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 14 (char 790)", "raw": null }, { "id": "grd-disulfide-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 18 column 3 (char 1062)", "raw": null }, { "id": "grd-disulfide-4ins", "prompt": "Load 4INS; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 18 column 1 (char 1055)", "raw": null }, { "id": "grd-ligand-1cbs-rea", "prompt": "Load 1CBS; show the protein as a grey cartoon and the REA as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 761)", "raw": null }, { "id": "grd-ligand-2hhb-hem", "prompt": "Load 2HHB; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 761)", "raw": null }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 22 column 14 (char 1554)", "raw": null }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 23 column 1 (char 1815)", "raw": null }, { "id": "int-004", "prompt": "Load 1A6M with the protein as a grey cartoon and show all the non-covalent interactions (hydrogen bonds, metal contacts) around the bound oxygen molecule.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 12 column 69 (char 870)", "raw": null }, { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 82 column 73 (char 6898)", "raw": null }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 93 column 93 (char 6647)", "raw": null }, { "id": "res-gfp", "prompt": "show green fluorescent protein from Aequorea victoria", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 16 column 1 (char 821)", "raw": null }, { "id": "res-lysozyme", "prompt": "Show me hen egg white lysozyme", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 20 column 1 (char 1350)", "raw": null }, { "id": "res-myoglobin", "prompt": "Show me sperm whale myoglobin", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1MBO.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 85 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick", "size_factor": 1.5 }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "label_comp_id": "HEM" } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick", "size_factor": 1.2 }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "component", "params": { "selector": "water" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick", "size_factor": 0.3 }, "children": [ { "kind": "color", "params": { "color": "lightblue" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 } } ] } ] } ] } ] } } }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 23 column 14 (char 1110)", "raw": null }, { "id": "res-pde5a", "prompt": "I wanna see a structure of PDE5A", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 22 column 1 (char 1352)", "raw": null } ] }, "qwen/qwen3-next-80b-a3b-instruct": { "outcomes": { "valid": 64, "unchecked": 0, "invalid_json": 3, "not_mvs": 0, "invalid_mvs": 3, "load_failed": 0 }, "n": 70, "mvs_f1": 0.8054, "failures": [ { "id": "named-1tup-248", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 248 and show it as blue ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Invalid parameters for node of kind \"component\":", " Missing required parameter \"selector\"." ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "auth_asym_id": "A", "auth_seq_id": 248 }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "blue" } } ] } ] } ] } ] } ] } ] } } }, { "id": "gen-focus-1cbs", "prompt": "Load 1CBS; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1cbs.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 } } ] } ] } ] } ] } } }, { "id": "gen-focus-1hho", "prompt": "Load 1HHO; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1hho.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 } } ] } ] } ] } ] } } }, { "id": "gen-ligands-1cbs", "prompt": "Load 1CBS; show the protein as a grey cartoon and the ligands as purple ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 663 (char 662)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1cbs.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"purple\"}}]}]}]}]}]}]}" }, { "id": "gen-ligands-1hho", "prompt": "Load 1HHO; show the protein as a grey cartoon and the ligands as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 660 (char 659)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}" }, { "id": "grd-ligand-1hho-hem", "prompt": "Load 1HHO; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 677 (char 676)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": {\"label_comp_id\": \"HEM\"}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}}" } ] }, "z-ai/glm-5.2": { "outcomes": { "valid": 63, "unchecked": 0, "invalid_json": 5, "not_mvs": 0, "invalid_mvs": 1, "load_failed": 1 }, "n": 70, "mvs_f1": 0.8052, "failures": [ { "id": "mvs-005", "prompt": "Load insulin (4INS) and render the protein as a steel-blue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 427 (char 426)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"steelblue\"}}]}]}]}]}]}}" }, { "id": "gen-focus-2hhb", "prompt": "Load 2HHB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 596 (char 595)", "raw": "```json\n{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}]},{\"kind\":\"focus\",\"params\":{}}]}]}]}]}]}}\n```" }, { "id": "grd-ligand-1hho-hem", "prompt": "Load 1HHO; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 614 (char 613)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"label_comp_id\":\"HEM\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}}" }, { "id": "grd-ligand-2hhb-hem", "prompt": "Load 2HHB; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 621 (char 620)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"label_comp_id\":\"HEM\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 26 column 1 (char 1667)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": [\n {\"auth_asym_id\": \"E\", \"auth_seq_id\": 57},\n {\"auth_asym_id\": \"E\", \"auth_seq_id\": 102},\n {\"auth_asym_id\": \"E\", \"auth_seq_id\": 195}\n ]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"#FFCC00\"}}]}]},\n {\"kind\": \"primitives\", \"params\": {\"color\": \"yellow\", \"label_color\": \"yellow\"}, \"children\": [\n {\"kind\": \"primitive\", \"params\": {\"kind\": \"distance_measurement\",\n \"start\": {\"auth_asym_id\": \"E\", \"auth_seq_id\": 195, \"label_atom_id\": \"OG\"},\n \"end\": {\"auth_asym_id\": \"E\", \"auth_seq_id\": 57, \"label_atom_id\": \"NE2\"},\n \"radius\": 0.06, \"dash_length\": 0.15, \"label_template\": \"{{distance}} Å\"}}]},\n {\"kind\": \"primitive\", \"params\": {\"kind\": \"distance_measurement\",\n \"start\": {\"auth_asym_id\": \"E\", \"auth_seq_id\": 57, \"label_atom_id\": \"ND1\"},\n \"end\": {\"auth_asym_id\": \"E\", \"auth_seq_id\": 102, \"label_atom_id\": \"OD2\"},\n \"radius\": 0.06, \"dash_length\": 0.15, \"label_template\": \"{{distance}} Å\"}}]}\n ]}]}]}\n]}}" }, { "id": "int-004", "prompt": "Load 1A6M with the protein as a grey cartoon and show all the non-covalent interactions (hydrogen bonds, metal contacts) around the bound oxygen molecule.", "outcome": "load_failed", "load_error": "render failed: Error: FormatError\n at j_ (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7670:159)\n at Cwt (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7677:56875)\n at e.f (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7677:56472)\n at HJ (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:35:61538)\n at tG (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:35:60775)\n at lF.run (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7586:109461)\n at r4.runTask (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7586:123836)\n at tf (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7677:56495)\n at lY (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7675:29405)\n at e.loadMvsData (file:///home/danbolser/Build/MolBench/molbench/static/molstar/molstar.js:7713:39371)", "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1a6m.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": { "label_comp_id": "OXY" }, "custom": { "molstar_show_non_covalent_interactions": true, "molstar_non_covalent_interactions_radius_ang": 5 } } } ] } ] } ] } ] } } }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/6msm.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" }, "custom": { "molstar_color_theme_name": "secondary-structure" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "component", "params": { "selector": "ion" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } } ] }, "baseline-rules": { "outcomes": { "valid": 0, "unchecked": 0, "invalid_json": 67, "not_mvs": 3, "invalid_mvs": 0, "load_failed": 0 }, "n": 70, "mvs_f1": 0.0 } }, "spec_grounded": { "claude-haiku-4-5": { "outcomes": { "valid": 65, "unchecked": 0, "invalid_json": 0, "not_mvs": 0, "invalid_mvs": 5, "load_failed": 0 }, "n": 70, "mvs_f1": 0.8417, "failures": [ { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/9MXL.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "res-gfp", "prompt": "show green fluorescent protein from Aequorea victoria", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/6L27.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "green" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "res-lysozyme", "prompt": "Show me hen egg white lysozyme", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/2vb1.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "res-myoglobin", "prompt": "Show me sperm whale myoglobin", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/5YCE.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/7S5H.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } } ] }, "deepseek/deepseek-v3.2": { "outcomes": { "valid": 68, "unchecked": 0, "invalid_json": 0, "not_mvs": 0, "invalid_mvs": 2, "load_failed": 0 }, "n": 70, "mvs_f1": 0.8877, "failures": [ { "id": "clinvar-1tup-F109", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant F109V as red ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"color\" cannot appear as a child of \"component\". Allowed parents for \"color\" are: \"representation\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1TUP.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 109 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" } }, { "kind": "color", "params": { "color": "red" } } ] } ] } ] } ] } ] } } }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/7S5H.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" }, "custom": { "molstar_color_theme_name": "secondary-structure" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 } } ] } ] } ] } ] } } } ] }, "deepseek/deepseek-v4-flash": { "outcomes": { "valid": 59, "unchecked": 0, "invalid_json": 11, "not_mvs": 0, "invalid_mvs": 0, "load_failed": 0 }, "n": 70, "mvs_f1": 0.7778, "failures": [ { "id": "mvs-001", "prompt": "Load haemoglobin (PDB 1HHO) and show the protein as a grey cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 462 (char 461)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}]}]}]}]}]}" }, { "id": "mvs-004", "prompt": "Load HIV-1 protease (1HVR); protein as grey cartoon, the bound inhibitor as magenta ball-and-stick, and focus the camera on the inhibitor.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 659 (char 658)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hvr.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"XK2\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\"}]}]}]}]}]}]}" }, { "id": "clinvar-1tup-F109", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant F109V as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 500 (char 499)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1TUP.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 109}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}]}" }, { "id": "hotspots-1tup", "prompt": "In p53 (PDB 1TUP), chain A, highlight the 6 mutational hotspot residues — the positions carrying the most pathogenic ClinVar variants — as red spheres.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "gen-chain-1lyz", "prompt": "Load 1LYZ; show everything as a grey cartoon, then colour chain A green.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 542 (char 541)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1lyz.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"all\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}, {\"kind\": \"color\", \"params\": {\"color\": \"green\", \"selector\": {\"auth_asym_id\": \"A\"}}}]}]}]}]}]}]}]}" }, { "id": "gen-focus-3ptb", "prompt": "Load 3PTB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 683 (char 682)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}, {\"kind\": \"focus\"}]}]}]}]}]}]}" }, { "id": "gen-ligands-3ptb", "prompt": "Load 3PTB; show the protein as a grey cartoon and the ligands as orange ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "gen-range-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show residues 50-110 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 723 (char 722)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"beg_auth_seq_id\": 50, \"end_auth_seq_id\": 110}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}]}]}" }, { "id": "int-002", "prompt": "Load 1A6M with the protein as a grey cartoon. Show the heme and the proximal histidine as ball-and-stick and measure the distance from the heme iron to the histidine's coordinating nitrogen.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" } ] }, "gemini-3.5-flash": { "outcomes": { "valid": 63, "unchecked": 0, "invalid_json": 5, "not_mvs": 0, "invalid_mvs": 2, "load_failed": 0 }, "n": 70, "mvs_f1": 0.816, "failures": [ { "id": "hotspots-1tup", "prompt": "In p53 (PDB 1TUP), chain A, highlight the 6 mutational hotspot residues — the positions carrying the most pathogenic ClinVar variants — as red spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 184 (char 183)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model" }, { "id": "gen-range-4ins", "prompt": "Load 4INS; protein as grey cartoon, and show residues 5-25 of chain B as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 466 (char 465)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/4ins.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\", \"beg_auth_seq_id\": 5, \"end_auth_seq_id\": 25}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}]}]}}" }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 184 (char 183)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1a6m.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\":" }, { "id": "int-002", "prompt": "Load 1A6M with the protein as a grey cartoon. Show the heme and the proximal histidine as ball-and-stick and measure the distance from the heme iron to the histidine's coordinating nitrogen.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 9 column 10 (char 177)", "raw": "```json\n{\n \"root\": {\n \"kind\": \"root\",\n \"children\": [\n {\n \"kind\": \"download\",\n \"params\": {\n \"url\": \"https://files.rcsb.org/download/1a6m.cif\"\n },\n \"children\": [\n {\n " }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "\n```\nWait, the prompt asks to show \"lengths\". Yes, distance_measurement will display it.\nWhat about focusing on the catalytic triad? It's usually good to add a `focus` node for the catalytic triad component, but the user didn't explicitly ask to focus. It says \"show ...\". Let's add a `focus` on the catalytic triad component so" }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/9mxl.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "white" }, "custom": { "molstar_color_theme_name": "chain-id" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/7s5h.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "assembly" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" }, "custom": { "molstar_color_theme_name": "chain-id" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "gray" }, "custom": { "molstar_color_theme_name": "element-symbol" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } } ] }, "google/gemma-3-27b-it": { "outcomes": { "valid": 49, "unchecked": 0, "invalid_json": 9, "not_mvs": 0, "invalid_mvs": 12, "load_failed": 0 }, "n": 70, "mvs_f1": 0.6538, "failures": [ { "id": "mvs-004", "prompt": "Load HIV-1 protease (1HVR); protein as grey cartoon, the bound inhibitor as magenta ball-and-stick, and focus the camera on the inhibitor.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1hvr.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "label_comp_id": "XK2" } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "label_comp_id": "XK2" } } } ] } ] } ] } ] } ] } } }, { "id": "clinvar-1tup-D281", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant D281Y as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting value: line 8 column 8 (char 433)", "raw": "```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}},\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 281}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}\n ]}\n ]}]}]}\n]}}\n```" }, { "id": "clinvar-1tup-F109", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant F109V as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 11 column 8 (char 699)", "raw": "```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 109}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]\n ]}\n ]}]}]}\n]}}\n```" }, { "id": "clinvar-1tup-N239", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant N239T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 9 column 3 (char 545)", "raw": "\n```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1TUP.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 239}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}\n]}}\n```" }, { "id": "clinvar-1tup-S215", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S215T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 12 column 1 (char 706)", "raw": "\n```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 215}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}\n ]}]}]}\n]}}\n```" }, { "id": "hotspots-1tup", "prompt": "In p53 (PDB 1TUP), chain A, highlight the 6 mutational hotspot residues — the positions carrying the most pathogenic ClinVar variants — as red spheres.", "outcome": "invalid_mvs", "mvs_issues": [ "Invalid parameters for node of kind \"representation\":", " Invalid value for parameter \"type\":", " \"sphere\" is not a valid value for literal type (\"cartoon\" | \"backbone\" | \"ball_and_stick\" | \"line\" | \"spacefill\" | \"carbohydrate\" | \"surface\" | \"putty\")" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": [ { "auth_asym_id": "A", "auth_seq_id": 109 } ] }, "children": [ { "kind": "representation", "params": { "type": "sphere" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "component", "params": { "selector": [ { "auth_asym_id": "A", "auth_seq_id": 110 } ] }, "children": [ { "kind": "representation", "params": { "type": "sphere" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "component", "params": { "selector": [ { "auth_asym_id": "A", "auth_seq_id": 158 } ] }, "children": [ { "kind": "representation", "params": { "type": "sphere" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "component", "params": { "selector": [ { "auth_asym_id": "A", "auth_seq_id": 179 } ] }, "children": [ { "kind": "representation", "params": { "type": "sphere" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "component", "params": { "selector": [ { "auth_asym_id": "A", "auth_seq_id": 215 } ] }, "children": [ { "kind": "representation", "params": { "type": "sphere" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "component", "params": { "selector": [ { "auth_asym_id": "A", "auth_seq_id": 238 } ] }, "children": [ { "kind": "representation", "params": { "type": "sphere" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "component", "params": { "selector": [ { "auth_asym_id": "A", "auth_seq_id": 239 } ] }, "children": [ { "kind": "representation", "params": { "type": "sphere" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "component", "params": { "selector": [ { "auth_asym_id": "A", "auth_seq_id": 240 } ] }, "children": [ { "kind": "representation", "params": { "type": "sphere" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "component", "params": { "selector": [ { "auth_asym_id": "A", "auth_seq_id": 241 } ] }, "children": [ { "kind": "representation", "params": { "type": "sphere" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] } ] } ] } ] } ] } } }, { "id": "gen-chain-3ptb", "prompt": "Load 3PTB; show everything as a grey cartoon, then colour chain A orange.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 14 column 3 (char 757)", "raw": "\n```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}\n ]}]}\n]}}\n```" }, { "id": "gen-chain-4ins", "prompt": "Load 4INS; show everything as a grey cartoon, then colour chain B blue.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 15 column 1 (char 771)", "raw": "\n```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/4ins.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}\n ]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"blue\"}}]}\n ]}\n ]}]}]}\n]}}\n```" }, { "id": "gen-focus-1cbs", "prompt": "Load 1CBS; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1cbs.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 5.0 }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 200 } } } ] } ] } ] } ] } ] } } }, { "id": "gen-focus-1hho", "prompt": "Load 1HHO; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1hho.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 } } ] } ] } ] } ] } } }, { "id": "gen-focus-2hhb", "prompt": "Load 2HHB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/2hhb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 142 } } } ] } ] } ] } ] } ] } } }, { "id": "gen-focus-3ptb", "prompt": "Load 3PTB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/3ptb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "label_comp_id": "BEN" } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "label_comp_id": "BEN" } } } ] } ] } ] } ] } ] } } }, { "id": "gen-ions-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 15 column 1 (char 746)", "raw": "```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": \"ion\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"sphere\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"purple\"}}]}]}\n ]}]}\n ]}]}\n]}}\n```" }, { "id": "gen-ions-2hhb", "prompt": "Load 2HHB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_mvs", "mvs_issues": [ "Invalid parameters for node of kind \"representation\":", " Invalid value for parameter \"type\":", " \"sphere\" is not a valid value for literal type (\"cartoon\" | \"backbone\" | \"ball_and_stick\" | \"line\" | \"spacefill\" | \"carbohydrate\" | \"surface\" | \"putty\")" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/2hhb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ion" }, "children": [ { "kind": "representation", "params": { "type": "sphere" }, "children": [ { "kind": "color", "params": { "color": "purple" } } ] } ] } ] } ] } ] } ] } } }, { "id": "gen-ions-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_mvs", "mvs_issues": [ "Invalid parameters for node of kind \"representation\":", " Invalid value for parameter \"type\":", " \"sphere\" is not a valid value for literal type (\"cartoon\" | \"backbone\" | \"ball_and_stick\" | \"line\" | \"spacefill\" | \"carbohydrate\" | \"surface\" | \"putty\")" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/3ptb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ion" }, "children": [ { "kind": "representation", "params": { "type": "sphere" }, "children": [ { "kind": "color", "params": { "color": "purple" } } ] } ] } ] } ] } ] } ] } } }, { "id": "grd-ligand-4ins-zn", "prompt": "Load 4INS; show the protein as a grey cartoon and the ZN as orange ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Invalid parameters for node of kind \"component\":", " Invalid value for parameter \"selector\":", " \"nonpolymer\" is not a valid value for literal type (\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\")", " Invalid value \"nonpolymer\" supplied to : ((\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\") | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>)/1: { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }", " Invalid value \"nonpolymer\" supplied to : ((\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\") | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>)/2: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/4ins.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "nonpolymer" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] } ] } ] } ] } ] } } }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "JSON parse error: Expecting property name enclosed in double quotes: line 32 column 11 (char 2346)", "raw": "\n```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]},\n {\"kind\": \"component\", \"params\": {\"selector\": [{\"auth_asym_id\": \"A\", \"auth_seq_id\": 57}]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": [{\"auth_asym_id\": \"A\", \"auth_seq_id\": 102}]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": [{\"auth_asym_id\": \"A\", \"auth_seq_id\": 195}]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": [{\"auth_asym_id\": \"A\", \"auth_seq_id\": 57}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 102}]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"line\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"blue\"}}]}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": [{\"auth_asym_id\": \"A\", \"auth_seq_id\": 102}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 195}]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"line\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"blue\"}}]}\n ]},\n\n {\"kind\": \"primitives\", \"params\": {\"color\": \"yellow\", \"label_color\": \"yellow\"}, \"children\": [\n {\"kind\": \"primitive\", \"params\": {\"kind\": \"distance_measurement\",\n \"start\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 57, \"label_atom_id\": \"NE2\"},\n \"end\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 102, \"label_atom_id\": \"OD1\"},\n \"radius\": 0.06, \"dash_length\": 0.15, \"label_template\": \"{{distance}}\"}}],\n [\"kind\": \"primitive\", \"params\": {\"kind\": \"distance_measurement\",\n \"start\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 102, \"label_atom_id\": \"OD2\"},\n \"end\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 195, \"label_atom_id\": \"OG\"},\n \"radius\": 0.06, \"dash_length\": 0.15, \"label_template\": \"{{distance}}\"}}\n ]}\n ]}]}]}\n]}}\n```" }, { "id": "int-004", "prompt": "Load 1A6M with the protein as a grey cartoon and show all the non-covalent interactions (hydrogen bonds, metal contacts) around the bound oxygen molecule.", "outcome": "invalid_mvs", "mvs_issues": [ "Invalid parameters for node of kind \"representation\":", " Missing required parameter \"type\"." ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1a6m.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" } } ] }, { "kind": "component", "params": { "selector": "water" }, "children": [] }, { "kind": "component", "params": { "selector": "ligand", "auth_asym_id": "A", "label_comp_id": "OXY" }, "children": [ { "kind": "representation", "params": {}, "children": [ { "kind": "custom", "params": { "molstar_show_non_covalent_interactions": true, "molstar_non_covalent_interactions_radius_ang": 5 } } ] } ] } ] } ] } ] } ] } } }, { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "invalid_mvs", "mvs_issues": [ "Unknown node kind \"custom\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/3ptb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_comp_id": "BEN" } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" } } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_comp_id": "BEN" } }, "children": [ { "kind": "custom", "params": { "molstar_show_non_covalent_interactions": true, "molstar_non_covalent_interactions_radius_ang": 5 } } ] } ] } ] } ] } ] } } }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 19 column 3 (char 862)", "raw": "```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/9MXL.cif\"}, \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"steelblue\"}}\n ]},\n {\"kind\": \"opacity\", \"params\": {\"opacity\": 0.8}}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}\n ]}\n ]}\n ]}\n ]}\n ]}\n]}\n```" }, { "id": "res-pde5a", "prompt": "I wanna see a structure of PDE5A", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"representation\" cannot appear as a child of \"structure\". Allowed parents for \"representation\" are: \"component\", \"component_from_uri\", \"component_from_source\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tbf.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] } ] } ] } ] } } } ] }, "gpt-5.4-nano": { "outcomes": { "valid": 53, "unchecked": 0, "invalid_json": 12, "not_mvs": 0, "invalid_mvs": 5, "load_failed": 0 }, "n": 70, "mvs_f1": 0.6049, "failures": [ { "id": "clinvar-1tup-N239", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant N239T as red ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"color\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 239 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "red" }, "children": [ { "kind": "focus", "params": { "radius": 5 } }, { "kind": "label", "params": { "text": "N239T (ClinVar)", "label_size": 0.8 } } ] } ] } ] } ] } ] } ] } ] } } }, { "id": "clinvar-1tup-S215", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S215T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 544 (char 543)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":215}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"},\"focus\":{\"radius\":6},\"label\":{\"text\":\"p53 S215T (ClinVar) — A:215\"}}]}]}]}]}]}]}}}" }, { "id": "named-1tup-143", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 143 and show it as blue ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"color\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 143 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick", "size_factor": 1 }, "children": [ { "kind": "color", "params": { "color": "blue" }, "children": [ { "kind": "focus", "params": { "radius": 6 } } ] }, { "kind": "label", "params": { "text": "p53 Val143", "label_size": 0.8 } } ] } ] } ] } ] } ] } ] } } }, { "id": "named-1tup-175", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 175 and show it as blue ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"representation\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model", "model_index": 0 }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 175 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick", "size_factor": 1 }, "children": [ { "kind": "color", "params": { "color": "blue" }, "custom": {} }, { "kind": "focus", "params": { "radius": 6 } } ] }, { "kind": "label", "params": { "text": "p53 Arg175 (P04637)", "label_size": 0.8 } } ] } ] } ] } ] } ] } } }, { "id": "gen-cartoon-1cbs", "prompt": "Load cellular retinoic-acid binding protein (1CBS) and show the protein as a purple cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 508 (char 507)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\",\"custom\":{\"molstar_color_theme_name\":\"chain-id\"}}}]}]}]}]}]}]}}}" }, { "id": "gen-cartoon-1hho", "prompt": "Load haemoglobin (1HHO) and show the protein as a red cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 456 (char 455)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1HHO.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}}}" }, { "id": "gen-chain-1cbs", "prompt": "Load 1CBS; show everything as a grey cartoon, then colour chain A purple.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 707 (char 706)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"all\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"},\"custom\":{\"molstar_color_theme_name\":\"chain-id\"}}]}]}]}]}]}]}}}" }, { "id": "gen-focus-1hho", "prompt": "Load 1HHO; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Invalid parameters for node of kind \"component\":", " Invalid value for parameter \"selector\":", " \"nonpolymer\" is not a valid value for literal type (\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\")", " Invalid value \"nonpolymer\" supplied to : ((\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\") | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>)/1: { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }", " Invalid value \"nonpolymer\" supplied to : ((\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\") | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>)/2: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1hho.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model", "model_index": 0 }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon", "size_factor": 1 }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "nonpolymer" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick", "size_factor": 1 }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "component", "params": { "selector": [ { "auth_asym_id": "A", "auth_seq_id": 150 }, { "auth_asym_id": "B", "auth_seq_id": 150 } ] }, "children": [ { "kind": "focus", "params": { "radius": 6 } } ] } ] } ] } ] } ] } } }, { "id": "gen-ions-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 687 (char 686)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":480}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}]}}}" }, { "id": "gen-range-1cbs", "prompt": "Load 1CBS; protein as grey cartoon, and show residues 20-60 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 695 (char 694)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":20,\"end_auth_seq_id\":60}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}}}" }, { "id": "gen-surface-4ins", "prompt": "Load 4INS; render the protein as a salmon molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 702 (char 701)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"salmon\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\",\"custom\":{\"molstar_color_theme_name\":\"chain-id\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"salmon\"}}]}]}]}]}]}]}}}" }, { "id": "grd-disulfide-1lyz", "prompt": "Load 1LYZ; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 879 (char 878)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":6},{\"auth_asym_id\":\"A\",\"auth_seq_id\":127},{\"auth_asym_id\":\"A\",\"auth_seq_id\":30},{\"auth_asym_id\":\"A\",\"auth_seq_id\":115},{\"auth_asym_id\":\"A\",\"auth_seq_id\":42},{\"auth_asym_id\":\"A\",\"auth_seq_id\":103}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"yellow\"}}]}]}]}]}]}]}]}}" }, { "id": "grd-disulfide-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 791 (char 790)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":56},{\"auth_asym_id\":\"A\",\"auth_seq_id\":114},{\"auth_asym_id\":\"A\",\"auth_seq_id\":187},{\"auth_asym_id\":\"A\",\"auth_seq_id\":189}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1.0},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"yellow\"}}]}]}]}]}]}]}}}" }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 1324 (char 1323)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1A6M.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":64}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":157,\"auth_comp_id\":\"OXY\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":64,\"auth_comp_id\":\"HIS\",\"label_atom_id\":\"NE2\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":157,\"label_comp_id\":\"OXY\",\"label_atom_id\":\"O2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}]}]}]}]}]}}}" }, { "id": "int-002", "prompt": "Load 1A6M with the protein as a grey cartoon. Show the heme and the proximal histidine as ball-and-stick and measure the distance from the heme iron to the histidine's coordinating nitrogen.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 1331 (char 1330)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"label_comp_id\":\"HEM\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":64,\"label_comp_id\":\"HIS\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"yellow\"}}]}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"white\",\"label_color\":\"white\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":154,\"label_comp_id\":\"HEM\",\"label_atom_id\":\"FE\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":64,\"label_comp_id\":\"HIS\",\"label_atom_id\":\"NE2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}]}]}]}]}]}}]}" }, { "id": "int-006", "prompt": "Load haemoglobin 1HHO; show the protein as a 50% transparent surface and the heme groups as ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1hho.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model", "model_index": 0 }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "surface", "size_factor": 1 }, "children": [ { "kind": "color", "params": { "color": "lightgray" } }, { "kind": "opacity", "params": { "opacity": 0.5 } } ] } ] }, { "kind": "component", "params": { "selector": [ { "auth_asym_id": "A", "auth_comp_id": "HEM" }, { "auth_asym_id": "B", "auth_comp_id": "HEM" } ] }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick", "size_factor": 1.2 }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "focus", "params": { "radius": 35 } } ] } ] } ] } ] } } }, { "id": "res-myoglobin", "prompt": "Show me sperm whale myoglobin", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 1 column 958 (char 957)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/5yce.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"slategray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"HEM\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"HEM\",\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"focus\",\"params\":{\"radius\":6}}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":35}},\"children\":[{\"kind\":\"label\",\"params\":{\"text\":\"Heme vicinity\"}}]}]}]}]}]}}}" } ] }, "meta-llama/llama-4-maverick": { "outcomes": { "valid": 58, "unchecked": 0, "invalid_json": 1, "not_mvs": 0, "invalid_mvs": 11, "load_failed": 0 }, "n": 70, "mvs_f1": 0.7927, "failures": [ { "id": "clinvar-1tup-F109", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant F109V as red ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 109 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 109 } } } ] } ] } ] } ] } ] } } }, { "id": "named-1tup-143", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 143 and show it as blue ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 143 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "blue" } } ] } ] }, { "kind": "focus", "params": {} } ] } ] } ] } ] } } }, { "id": "named-1tup-175", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 175 and show it as blue ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 175 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "blue" } } ] } ] }, { "kind": "focus", "params": {} } ] } ] } ] } ] } } }, { "id": "gen-focus-1cbs", "prompt": "Load 1CBS; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1cbs.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": { "label_comp_id": "REA" } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] }, { "kind": "focus" } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "gen-focus-2hhb", "prompt": "Load 2HHB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/2hhb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] }, { "kind": "focus" } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/3ptb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "grey" } } ] } ] }, { "kind": "component", "params": { "selector": [ { "auth_asym_id": "A", "auth_seq_id": 57 }, { "auth_asym_id": "A", "auth_seq_id": 102 }, { "auth_asym_id": "A", "auth_seq_id": 195 } ] }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "primitives", "params": { "color": "yellow", "label_color": "yellow" }, "children": [ { "kind": "primitive", "params": { "kind": "distance_measurement", "start": { "auth_asym_id": "A", "auth_seq_id": 102, "label_atom_id": "OD1" }, "end": { "auth_asym_id": "A", "auth_seq_id": 57, "label_atom_id": "ND1" }, "radius": 0.06, "dash_length": 0.15, "label_template": "{{distance}}" } }, { "kind": "primitive", "params": { "kind": "distance_measurement", "start": { "auth_asym_id": "A", "auth_seq_id": 57, "label_atom_id": "NE2" }, "end": { "auth_asym_id": "A", "auth_seq_id": 195, "label_atom_id": "OG" }, "radius": 0.06, "dash_length": 0.15, "label_template": "{{distance}}" } } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 17 column 3 (char 812)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"BEN\"}}, \"children\": [\n {\"kind\": \"custom\", \"params\": {\"molstar_show_non_covalent_interactions\": true, \"molstar_non_covalent_interactions_radius_ang\": 5}}\n ]}\n ]}\n ]}\n ]}\n ]}\n]}" }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/9MXL.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "lightblue" } } ] } ] }, { "kind": "focus", "params": {} } ] } ] } ] } ] } } }, { "id": "res-gfp", "prompt": "show green fluorescent protein from Aequorea victoria", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/6L27.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "green" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "res-lysozyme", "prompt": "Show me hen egg white lysozyme", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/2vb1.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "res-myoglobin", "prompt": "Show me sperm whale myoglobin", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/5YCE.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "res-pde5a", "prompt": "I wanna see a structure of PDE5A", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tbf.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } } ] }, "minimax/minimax-m3": { "outcomes": { "valid": 64, "unchecked": 0, "invalid_json": 3, "not_mvs": 0, "invalid_mvs": 3, "load_failed": 0 }, "n": 70, "mvs_f1": 0.8188, "failures": [ { "id": "gen-chain-4ins", "prompt": "Load 4INS; show everything as a grey cartoon, then colour chain B blue.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 602 (char 601)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"blue\"}}]}]}]}]}]}]}}" }, { "id": "gen-ions-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Extra data: line 13 column 1 (char 746)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": \"ion\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"spacefill\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"purple\"}}]}]}\n ]}]}]\n }]}}\n}" }, { "id": "grd-disulfide-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "res-gfp", "prompt": "show green fluorescent protein from Aequorea victoria", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/2wur.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "#00C800" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "yellow" } } ] } ] }, { "kind": "focus", "params": { "radius": 30 } } ] } ] } ] } ] } } }, { "id": "res-lysozyme", "prompt": "Show me hen egg white lysozyme", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/2vb1.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "white" }, "custom": { "molstar_color_theme_name": "sequence-id" } } ] } ] }, { "kind": "focus", "params": { "radius": 30 } } ] } ] } ] } ] } } }, { "id": "res-myoglobin", "prompt": "Show me sperm whale myoglobin", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1a6m.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": { "label_comp_id": "HEM" } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "component", "params": { "selector": { "label_comp_id": "OXY" } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "red" } } ] } ] }, { "kind": "focus", "params": { "radius": 12 } } ] } ] } ] } ] } } } ] }, "moonshotai/kimi-k2.6": { "outcomes": { "valid": 45, "unchecked": 0, "invalid_json": 24, "not_mvs": 0, "invalid_mvs": 1, "load_failed": 0 }, "n": 70, "mvs_f1": 0.5676, "failures": [ { "id": "mvs-004", "prompt": "Load HIV-1 protease (1HVR); protein as grey cartoon, the bound inhibitor as magenta ball-and-stick, and focus the camera on the inhibitor.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 675 (char 674)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hvr.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":263,\"auth_comp_id\":\"XK2\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\"}]}]}]}]}}]}}" }, { "id": "clinvar-1tup-D281", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant D281Y as red ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "clinvar-1tup-N239", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant N239T as red ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "clinvar-1tup-S215", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S215T as red ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "clinvar-1tup-S241", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S241Y as red ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "gen-chain-1cbs", "prompt": "Load 1CBS; show everything as a grey cartoon, then colour chain A purple.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "gen-chain-1lyz", "prompt": "Load 1LYZ; show everything as a grey cartoon, then colour chain A green.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "gen-chain-3ptb", "prompt": "Load 3PTB; show everything as a grey cartoon, then colour chain A orange.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "gen-chain-4ins", "prompt": "Load 4INS; show everything as a grey cartoon, then colour chain B blue.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "gen-focus-3ptb", "prompt": "Load 3PTB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "gen-ligands-2hhb", "prompt": "Load 2HHB; show the protein as a grey cartoon and the ligands as teal ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "gen-ligands-3ptb", "prompt": "Load 3PTB; show the protein as a grey cartoon and the ligands as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 661 (char 660)", "raw": " {\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}}]}}" }, { "id": "gen-range-1cbs", "prompt": "Load 1CBS; protein as grey cartoon, and show residues 20-60 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 15 column 9 (char 842)", "raw": " {\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1cbs.cif\"}, \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}\n ]}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"beg_auth_seq_id\": 20, \"end_auth_seq_id\": 60}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}\n ]}\n ]}\n ]}}\n ]}\n ]}}\n]}}" }, { "id": "gen-range-1lyz", "prompt": "Load 1LYZ; protein as grey cartoon, and show residues 40-80 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 720 (char 719)", "raw": " {\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1lyz.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"beg_auth_seq_id\": 40, \"end_auth_seq_id\": 80}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}}]}}" }, { "id": "gen-range-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show residues 50-110 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "grd-disulfide-1lyz", "prompt": "Load 1LYZ; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 990 (char 989)", "raw": " {\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1lyz.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": [{\"auth_asym_id\": \"A\", \"auth_seq_id\": 6}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 30}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 64}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 76}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 80}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 94}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 115}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 127}]}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"yellow\"}}]}]}]}]}]}}]}}" }, { "id": "grd-disulfide-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "grd-ligand-1cbs-rea", "prompt": "Load 1CBS; show the protein as a grey cartoon and the REA as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 694 (char 693)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1cbs.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 200}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}}]}" }, { "id": "grd-ligand-2hhb-hem", "prompt": "Load 2HHB; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 677 (char 676)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/2hhb.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": {\"label_comp_id\": \"HEM\"}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}}]}}" }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "int-002", "prompt": "Load 1A6M with the protein as a grey cartoon. Show the heme and the proximal histidine as ball-and-stick and measure the distance from the heme iron to the histidine's coordinating nitrogen.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 184 (char 183)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1a6m.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children" }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "int-004", "prompt": "Load 1A6M with the protein as a grey cartoon and show all the non-covalent interactions (hydrogen bonds, metal contacts) around the bound oxygen molecule.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/7s5h.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "lightblue" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "component", "params": { "selector": "ion" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "green" } } ] } ] }, { "kind": "focus", "params": {} } ] } ] } ] } ] } } } ] }, "nvidia/nemotron-3-super-120b-a12b": { "outcomes": { "valid": 6, "unchecked": 0, "invalid_json": 63, "not_mvs": 0, "invalid_mvs": 1, "load_failed": 0 }, "n": 70, "mvs_f1": 0.081, "failures": [ { "id": "mvs-001", "prompt": "Load haemoglobin (PDB 1HHO) and show the protein as a grey cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 424 (char 423)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]}]}]}]}]}]}" }, { "id": "mvs-002", "prompt": "Load haemoglobin (1HHO); show the protein as a grey cartoon and the heme groups as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 622 (char 621)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1HHO.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"HEM\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}" }, { "id": "mvs-003", "prompt": "Load hen egg-white lysozyme (1LYZ) as a grey cartoon, and show the two catalytic residues Glu35 and Asp52 on chain A as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 674 (char 673)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":35},{\"auth_asym_id\":\"A\",\"auth_seq_id\":52}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}]}]}}" }, { "id": "mvs-004", "prompt": "Load HIV-1 protease (1HVR); protein as grey cartoon, the bound inhibitor as magenta ball-and-stick, and focus the camera on the inhibitor.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 626 (char 625)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hvr.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\"}]}]}]}]}]}]}\"}]}" }, { "id": "clinvar-1tup-D281", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant D281Y as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 459 (char 458)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":281}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}]}}" }, { "id": "clinvar-1tup-F109", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant F109V as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 459 (char 458)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":109}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}]}}" }, { "id": "clinvar-1tup-N239", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant N239T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 500 (char 499)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 239}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}]}" }, { "id": "clinvar-1tup-S215", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S215T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 636 (char 635)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":215}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}]}}" }, { "id": "clinvar-1tup-S241", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S241Y as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 460 (char 459)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":241}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}]}" }, { "id": "hotspots-1tup", "prompt": "In p53 (PDB 1TUP), chain A, highlight the 6 mutational hotspot residues — the positions carrying the most pathogenic ClinVar variants — as red spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 397 (char 396)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":16},{\"auth_asym_id\":\"A\",\"auth_seq_id\":17},{\"auth_asym_id\":\"A\",\"auth_seq_id\":122},{\"auth_asym_id\":\"A\",\"auth_seq_id\":146" }, { "id": "named-1tup-143", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 143 and show it as blue ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 460 (char 459)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":143}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"blue\"}}]}]}]}]}]}]}]}" }, { "id": "named-1tup-175", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 175 and show it as blue ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 460 (char 459)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":175}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"blue\"}}]}]}]}]}]}]}]}" }, { "id": "named-1tup-248", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 248 and show it as blue ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 460 (char 459)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":248}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"blue\"}}]}]}]}]}]}]}]}" }, { "id": "gen-cartoon-1cbs", "prompt": "Load cellular retinoic-acid binding protein (1CBS) and show the protein as a purple cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 464 (char 463)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1cbs.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"purple\"}}]}]}]}]}]}]}]}" }, { "id": "gen-cartoon-1hho", "prompt": "Load haemoglobin (1HHO) and show the protein as a red cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 461 (char 460)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}]}" }, { "id": "gen-cartoon-1lyz", "prompt": "Load lysozyme (1LYZ) and show the protein as a green cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 425 (char 424)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"green\"}}]}]}]}]}]}]}]}" }, { "id": "gen-cartoon-2hhb", "prompt": "Load deoxyhaemoglobin (2HHB) and show the protein as a teal cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 462 (char 461)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/2hhb.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"teal\"}}]}]}]}]}]}]}]}" }, { "id": "gen-cartoon-3ptb", "prompt": "Load trypsin (3PTB) and show the protein as a orange cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 464 (char 463)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}]}]}]}" }, { "id": "gen-cartoon-4ins", "prompt": "Load insulin (4INS) and show the protein as a blue cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 462 (char 461)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/4ins.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"blue\"}}]}]}]}]}]}]}]}" }, { "id": "gen-chain-1cbs", "prompt": "Load 1CBS; show everything as a grey cartoon, then colour chain A purple.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 501 (char 500)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}},{\"kind\":\"color\",\"params\":{\"color\":\"purple\"},\"selector\":{\"auth_asym_id\":\"A\"}}]}]}]}]}]}]}]}]}}" }, { "id": "gen-chain-1hho", "prompt": "Load 1HHO; show everything as a grey cartoon, then colour chain A red.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 610 (char 609)", "raw": "\n\n{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}]}" }, { "id": "gen-chain-1lyz", "prompt": "Load 1LYZ; show everything as a grey cartoon, then colour chain A green.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 500 (char 499)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}},{\"kind\":\"color\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"},\"color\":\"green\"}}]}]}]}]}]}]}]}}" }, { "id": "gen-chain-2hhb", "prompt": "Load 2HHB; show everything as a grey cartoon, then colour chain B teal.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 611 (char 610)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"teal\"}}]}]}]}]}]}]}]}" }, { "id": "gen-chain-3ptb", "prompt": "Load 3PTB; show everything as a grey cartoon, then colour chain A orange.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 614 (char 613)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}" }, { "id": "gen-chain-4ins", "prompt": "Load 4INS; show everything as a grey cartoon, then colour chain B blue.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 667 (char 666)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/4ins.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\"}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"blue\"}}]}]}]}]}]}]}]}" }, { "id": "gen-focus-1cbs", "prompt": "Load 1CBS; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 668 (char 667)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":200}},\"children\":[{\"kind\":\"focus\",\"params\":{}},{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]}]}]}]}]}]}]}" }, { "id": "gen-focus-3ptb", "prompt": "Load 3PTB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 638 (char 637)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\",\"params\":{}}]}]}]}]}]}]}]}}" }, { "id": "gen-ions-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 600 (char 599)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1HHO.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ion\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}]}]}" }, { "id": "gen-ions-2hhb", "prompt": "Load 2HHB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 617 (char 616)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"PO4\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}]}]}" }, { "id": "gen-ions-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 635 (char 634)", "raw": "\n\n{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"CA\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}]}]}" }, { "id": "gen-ions-4ins", "prompt": "Load 4INS; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 655 (char 654)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/4ins.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"grey\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": \"ion\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"spacefill\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"purple\"}}]}]}]}]}]}]}]}" }, { "id": "gen-ligands-1cbs", "prompt": "Load 1CBS; show the protein as a grey cartoon and the ligands as purple ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 639 (char 638)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":200}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}]}]}" }, { "id": "gen-ligands-1hho", "prompt": "Load 1HHO; show the protein as a grey cartoon and the ligands as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 660 (char 659)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}]}" }, { "id": "gen-ligands-2hhb", "prompt": "Load 2HHB; show the protein as a grey cartoon and the ligands as teal ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 610 (char 609)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"nonpolymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"teal\"}}]}]}]}]}]}]}]}\"}" }, { "id": "gen-ligands-3ptb", "prompt": "Load 3PTB; show the protein as a grey cartoon and the ligands as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 608 (char 607)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}" }, { "id": "gen-range-1cbs", "prompt": "Load 1CBS; protein as grey cartoon, and show residues 20-60 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 662 (char 661)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":20,\"end_auth_seq_id\":60}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}" }, { "id": "gen-range-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show residues 30-90 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 662 (char 661)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":30,\"end_auth_seq_id\":90}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}}" }, { "id": "gen-range-1lyz", "prompt": "Load 1LYZ; protein as grey cartoon, and show residues 40-80 of chain A as orange ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Invalid parameters for node of kind \"component\":", " Invalid value for parameter \"selector\":", " \"[object Object]\" is not a valid value for literal type (\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\")", " Invalid value {\"beg\":40,\"end\":80} supplied to : ((\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\") | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>)/1: { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }/auth_seq_id: Integer", " Invalid value {\"auth_asym_id\":\"A\",\"auth_seq_id\":{\"beg\":40,\"end\":80}} supplied to : ((\"all\" | \"polymer\" | \"protein\" | \"nucleic\" | \"branched\" | \"ligand\" | \"ion\" | \"water\" | \"coarse\") | { label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string } | Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>)/2: Array<{ label_entity_id?: string, label_asym_id?: string, auth_asym_id?: string, label_seq_id?: Integer, auth_seq_id?: Integer, pdbx_PDB_ins_code?: string, beg_label_seq_id?: Integer, end_label_seq_id?: Integer, beg_auth_seq_id?: Integer, end_auth_seq_id?: Integer, label_comp_id?: string, auth_comp_id?: string, residue_index?: Integer, label_atom_id?: string, auth_atom_id?: string, type_symbol?: string, atom_id?: Integer, atom_index?: Integer, instance_id?: string }>" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1lyz.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "grey" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": { "beg": 40, "end": 80 } } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] } ] } ] } ] } ] } } }, { "id": "gen-range-2hhb", "prompt": "Load 2HHB; protein as grey cartoon, and show residues 10-70 of chain B as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 663 (char 662)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\",\"beg_auth_seq_id\":10,\"end_auth_seq_id\":70}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}}" }, { "id": "gen-range-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show residues 50-110 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 664 (char 663)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":50,\"end_auth_seq_id\":110}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}]}" }, { "id": "gen-range-4ins", "prompt": "Load 4INS; protein as grey cartoon, and show residues 5-25 of chain B as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 661 (char 660)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\",\"beg_auth_seq_id\":5,\"end_auth_seq_id\":25}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}]}}" }, { "id": "gen-surface-1cbs", "prompt": "Load 1CBS; render the protein as a steelblue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 429 (char 428)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"steelblue\"}}]}]}]}]}]}]}]}" }, { "id": "gen-surface-1hho", "prompt": "Load 1HHO; render the protein as a steelblue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 429 (char 428)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"steelblue\"}}]}]}]}]}]}]}]}" }, { "id": "gen-surface-1lyz", "prompt": "Load 1LYZ; render the protein as a khaki molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 425 (char 424)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"khaki\"}}]}]}]}]}]}]}]}]}}" }, { "id": "gen-surface-2hhb", "prompt": "Load 2HHB; render the protein as a salmon molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 426 (char 425)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"salmon\"}}]}]}]}]}]}]}]}}" }, { "id": "gen-surface-4ins", "prompt": "Load 4INS; render the protein as a salmon molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 426 (char 425)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"salmon\"}}]}]}]}]}]}]}]}\"}" }, { "id": "grd-disulfide-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 623 (char 622)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"CYS\"}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"yellow\"}}]}]}]}]}]}]}]}" }, { "id": "grd-disulfide-4ins", "prompt": "Load 4INS; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "grd-ligand-1cbs-rea", "prompt": "Load 1CBS; show the protein as a grey cartoon and the REA as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 618 (char 617)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"}},{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"label_asym_id\":\"B\",\"label_comp_id\":\"REA\"}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"}},{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}}" }, { "id": "grd-ligand-1hho-hem", "prompt": "Load 1HHO; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 678 (char 677)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_comp_id\": \"HEM\"}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}]}]}" }, { "id": "grd-ligand-2hhb-hem", "prompt": "Load 2HHB; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 678 (char 677)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/2hhb.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_comp_id\": \"HEM\"}}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}]}]}" }, { "id": "grd-ligand-4ins-zn", "prompt": "Load 4INS; show the protein as a grey cartoon and the ZN as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 622 (char 621)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"ZN\"}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}" }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1025 (char 1024)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":64},{\"auth_asym_id\":\"A\",\"auth_seq_id\":157}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":64,\"label_atom_id\":\"NE2\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":157,\"label_atom_id\":\"O2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}]}]}]}]}]}]}" }, { "id": "int-002", "prompt": "Load 1A6M with the protein as a grey cartoon. Show the heme and the proximal histidine as ball-and-stick and measure the distance from the heme iron to the histidine's coordinating nitrogen.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1201 (char 1200)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"HEM\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":93}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"cyan\"}}]}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"HEM\",\"auth_atom_id\":\"FE\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":93,\"label_atom_id\":\"NE2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}]}]}]}]}]}]}" }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1268 (char 1267)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":57},{\"auth_asym_id\":\"A\",\"auth_seq_id\":102},{\"auth_asym_id\":\"A\",\"auth_seq_id\":195}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"}}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":57,\"label_atom_id\":\"ND1\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":102,\"label_atom_id\":\"OD1\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}},{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":57,\"label_atom_id\":\"NE2\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":195,\"label_atom_id\":\"OG\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}]}]}]}]}]}]}}" }, { "id": "int-004", "prompt": "Load 1A6M with the protein as a grey cartoon and show all the non-covalent interactions (hydrogen bonds, metal contacts) around the bound oxygen molecule.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 615 (char 614)", "raw": "\n\n{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"grey\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"OXY\"}},\"custom\":{\"molstar_show_non_covalent_interactions\":true,\"molstar_non_covalent_interactions_radius_ang\":5}}]}]}]}]}]}]}" }, { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 615 (char 614)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"BEN\"}},\"custom\":{\"molstar_show_non_covalent_interactions\":true,\"molstar_non_covalent_interactions_radius_ang\":5}}]}]}]}]}]}]}}" }, { "id": "int-006", "prompt": "Load haemoglobin 1HHO; show the protein as a 50% transparent surface and the heme groups as ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 667 (char 666)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}},{\"kind\":\"opacity\",\"params\":{\"opacity\":0.5}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"HEM\"}}, \"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}]}" }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 515 (char 514)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/9mxl.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"white\"}, \"custom\": {\"molstar_color_theme_name\": \"chain-id\"}}]}]}]}]}]}]}]}" }, { "id": "res-gfp", "prompt": "show green fluorescent protein from Aequorea victoria", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 425 (char 424)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/6L27.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"green\"}}]}]}]}]}]}]}]}" }, { "id": "res-lysozyme", "prompt": "Show me hen egg white lysozyme", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 462 (char 461)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/2vb1.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}]}]}]}]}]}" }, { "id": "res-myoglobin", "prompt": "Show me sperm whale myoglobin", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 663 (char 662)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/5yce.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}, {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}]}]}]}]}]}]}}" }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 424 (char 423)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/7s5h.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]}]}]}]}]}]}" }, { "id": "res-pde5a", "prompt": "I wanna see a structure of PDE5A", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 462 (char 461)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tbf.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]}]}]}]}]}]}" } ] }, "openai/gpt-oss-120b": { "outcomes": { "valid": 46, "unchecked": 0, "invalid_json": 24, "not_mvs": 0, "invalid_mvs": 0, "load_failed": 0 }, "n": 70, "mvs_f1": 0.5817, "failures": [ { "id": "clinvar-1tup-S241", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S241Y as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 657 (char 656)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":241}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]},{\"kind\":\"focus\"}]}]}}]}]}}" }, { "id": "named-1tup-143", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 143 and show it as blue ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 494 (char 493)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [{\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"}, \"children\": [{\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [{\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [{\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 143}},\"children\": [{\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [{\"kind\": \"color\", \"params\": {\"color\": \"blue\"}}]}]}]}}]}]}]}}" }, { "id": "gen-cartoon-1lyz", "prompt": "Load lysozyme (1LYZ) and show the protein as a green cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 423 (char 422)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"green\"}}]}]}]}]}]}}]}}" }, { "id": "gen-chain-1cbs", "prompt": "Load 1CBS; show everything as a grey cartoon, then colour chain A purple.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 607 (char 606)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}}]}]}}" }, { "id": "gen-chain-2hhb", "prompt": "Load 2HHB; show everything as a grey cartoon, then colour chain B teal.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 609 (char 608)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"teal\"}}]}]}]}]}]}}}" }, { "id": "gen-focus-1cbs", "prompt": "Load 1CBS; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 650 (char 649)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":200}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\"}]}]}}]}]}}" }, { "id": "gen-ions-2hhb", "prompt": "Load 2HHB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 598 (char 597)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ion\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}}" }, { "id": "gen-ligands-1cbs", "prompt": "Load 1CBS; show the protein as a grey cartoon and the ligands as purple ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 636 (char 635)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":200}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}}" }, { "id": "gen-range-1cbs", "prompt": "Load 1CBS; protein as grey cartoon, and show residues 20-60 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 656 (char 655)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":20,\"end_auth_seq_id\":60}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}}]}]}}" }, { "id": "gen-range-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show residues 30-90 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 656 (char 655)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":30,\"end_auth_seq_id\":90}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}}]}]}}" }, { "id": "gen-range-2hhb", "prompt": "Load 2HHB; protein as grey cartoon, and show residues 10-70 of chain B as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 656 (char 655)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\",\"beg_auth_seq_id\":10,\"end_auth_seq_id\":70}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}}]}}]}}" }, { "id": "gen-range-4ins", "prompt": "Load 4INS; protein as grey cartoon, and show residues 5-25 of chain B as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 655 (char 654)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\",\"beg_auth_seq_id\":5,\"end_auth_seq_id\":25}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}}]}]}}" }, { "id": "grd-disulfide-1lyz", "prompt": "Load 1LYZ; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 900 (char 899)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":6},{\"auth_asym_id\":\"A\",\"auth_seq_id\":30},{\"auth_asym_id\":\"A\",\"auth_seq_id\":64},{\"auth_asym_id\":\"A\",\"auth_seq_id\":76},{\"auth_asym_id\":\"A\",\"auth_seq_id\":80},{\"auth_asym_id\":\"A\",\"auth_seq_id\":94},{\"auth_asym_id\":\"A\",\"auth_seq_id\":115},{\"auth_asym_id\":\"A\",\"auth_seq_id\":127}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"yellow\"}}]}]}]}}]}]}}" }, { "id": "grd-ligand-1hho-hem", "prompt": "Load 1HHO; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 677 (char 676)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":143},{\"auth_asym_id\":\"B\",\"auth_seq_id\":147}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}}" }, { "id": "grd-ligand-2hhb-hem", "prompt": "Load 2HHB; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 621 (char 620)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"label_comp_id\":\"HEM\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "grd-ligand-3ptb-ca", "prompt": "Load 3PTB; show the protein as a grey cartoon and the CA as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 636 (char 635)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":480}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}}" }, { "id": "grd-ligand-4ins-zn", "prompt": "Load 4INS; show the protein as a grey cartoon and the ZN as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 673 (char 672)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"B\",\"auth_seq_id\":101},{\"auth_asym_id\":\"D\",\"auth_seq_id\":101}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}}]}]}}" }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1192 (char 1191)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":64}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":157}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":64,\"label_atom_id\":\"NE2\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":157,\"label_atom_id\":\"O2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}]}]}}]}}]}" }, { "id": "int-002", "prompt": "Load 1A6M with the protein as a grey cartoon. Show the heme and the proximal histidine as ball-and-stick and measure the distance from the heme iron to the histidine's coordinating nitrogen.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1063 (char 1062)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":154,\"label_comp_id\":\"HEM\"},{\"auth_asym_id\":\"A\",\"auth_seq_id\":93,\"label_comp_id\":\"HIS\"}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":154,\"label_atom_id\":\"FE\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":93,\"label_atom_id\":\"ND1\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}}\"}}]}]}}]}]}}}" }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1076 (char 1075)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":57},{\"auth_asym_id\":\"A\",\"auth_seq_id\":102},{\"auth_asym_id\":\"A\",\"auth_seq_id\":195}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":57,\"label_atom_id\":\"NE2\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":102,\"label_atom_id\":\"OD1\"},\"color\":\"yellow\",\"radius\":0.06,\"dash_length\":0.12,\"label_template\":\"{{distance}}\"}},\"{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":102,\"label_atom_id\":\"OD2\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":195,\"label_atom_id\":\"OG\"},\"color\":\"yellow\",\"radius\":0.06,\"dash_length\":0.12,\"label_template\":\"{{distance}}\"}}]}}]}}]}}" }, { "id": "int-006", "prompt": "Load haemoglobin 1HHO; show the protein as a 50% transparent surface and the heme groups as ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 665 (char 664)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}},{\"kind\":\"opacity\",\"params\":{\"opacity\":0.5}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"label_comp_id\":\"HEM\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 471 (char 470)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/9mxl.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\",\"custom\":{\"molstar_color_theme_name\":\"chain-id\"}}}]},\"focus\":{\"params\":{}}]}]}}]}}]}}" }, { "id": "res-myoglobin", "prompt": "Show me sperm whale myoglobin", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 619 (char 618)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/5YCE.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]},{\"kind\":\"focus\"}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}}]}]}}}" }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 444 (char 443)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/7s5h.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"lightgray\"}}]},{\"kind\":\"focus\"}]}]}]}]}}}" } ] }, "openai/gpt-oss-20b": { "outcomes": { "valid": 17, "unchecked": 0, "invalid_json": 53, "not_mvs": 0, "invalid_mvs": 0, "load_failed": 0 }, "n": 70, "mvs_f1": 0.2066, "failures": [ { "id": "mvs-003", "prompt": "Load hen egg-white lysozyme (1LYZ) as a grey cartoon, and show the two catalytic residues Glu35 and Asp52 on chain A as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 672 (char 671)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":35},{\"auth_asym_id\":\"A\",\"auth_seq_id\":52}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}}" }, { "id": "mvs-004", "prompt": "Load HIV-1 protease (1HVR); protein as grey cartoon, the bound inhibitor as magenta ball-and-stick, and focus the camera on the inhibitor.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 683 (char 682)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hvr.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1.0},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"label_comp_id\":\"XK2\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1.0},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\",\"params\":{}}]}]}}]}]}}" }, { "id": "mvs-005", "prompt": "Load insulin (4INS) and render the protein as a steel-blue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 429 (char 428)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4INS.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"steelblue\"}}]}]}]}]}]}]}" }, { "id": "clinvar-1tup-D281", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant D281Y as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 735 (char 734)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1.0},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":281}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1.0},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]},{\"kind\":\"focus\",\"params\":{\"radius\":3}}]}]}]}}" }, { "id": "clinvar-1tup-N239", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant N239T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 459 (char 458)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1TUP.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":239}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}]}" }, { "id": "hotspots-1tup", "prompt": "In p53 (PDB 1TUP), chain A, highlight the 6 mutational hotspot residues — the positions carrying the most pathogenic ClinVar variants — as red spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 645 (char 644)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":215},{\"auth_asym_id\":\"A\",\"auth_seq_id\":109},{\"auth_asym_id\":\"A\",\"auth_seq_id\":281},{\"auth_asym_id\":\"A\",\"auth_seq_id\":110},{\"auth_asym_id\":\"A\",\"auth_seq_id\":239},{\"auth_asym_id\":\"A\",\"auth_seq_id\":241}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}}]}]}}" }, { "id": "named-1tup-248", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 248 and show it as blue ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 458 (char 457)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":248}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"blue\"}}]}]}]}]}]}}" }, { "id": "gen-cartoon-1cbs", "prompt": "Load cellular retinoic-acid binding protein (1CBS) and show the protein as a purple cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 424 (char 423)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}}" }, { "id": "gen-cartoon-2hhb", "prompt": "Load deoxyhaemoglobin (2HHB) and show the protein as a teal cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 422 (char 421)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"teal\"}}]}]}]}]}]}}" }, { "id": "gen-cartoon-4ins", "prompt": "Load insulin (4INS) and show the protein as a blue cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 422 (char 421)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"blue\"}}]}]}]}]}]}}" }, { "id": "gen-chain-1cbs", "prompt": "Load 1CBS; show everything as a grey cartoon, then colour chain A purple.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 611 (char 610)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}}" }, { "id": "gen-chain-1hho", "prompt": "Load 1HHO; show everything as a grey cartoon, then colour chain A red.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 608 (char 607)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]}]}]}]}]}}" }, { "id": "gen-chain-1lyz", "prompt": "Load 1LYZ; show everything as a grey cartoon, then colour chain A green.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 606 (char 605)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"all\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"green\"}}]}]}]}]}]}}" }, { "id": "gen-chain-3ptb", "prompt": "Load 3PTB; show everything as a grey cartoon, then colour chain A orange.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 611 (char 610)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-chain-4ins", "prompt": "Load 4INS; show everything as a grey cartoon, then colour chain B blue.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 497 (char 496)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}},{\"kind\":\"color\",\"params\":{\"color\":\"blue\",\"selector\":{\"auth_asym_id\":\"B\"}}}]}]}]}]}]}}" }, { "id": "gen-focus-1cbs", "prompt": "Load 1CBS; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 636 (char 635)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\",\"params\":{}}]}]}]}]}}" }, { "id": "gen-focus-1hho", "prompt": "Load 1HHO; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 810 (char 809)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":150,\"auth_comp_id\":\"OXY\"}},\"children\":[{\"kind\":\"focus\",\"params\":{\"radius\":5}}]}]}]}]}}" }, { "id": "gen-focus-2hhb", "prompt": "Load 2HHB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 624 (char 623)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\"}]}]}]}]}}" }, { "id": "gen-focus-3ptb", "prompt": "Load 3PTB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 624 (char 623)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\"}]}]}]}]}}" }, { "id": "gen-ions-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 631 (char 630)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":142}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}}" }, { "id": "gen-ions-2hhb", "prompt": "Load 2HHB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 649 (char 648)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"PO4\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}]}" }, { "id": "gen-ions-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 633 (char 632)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\",\"auth_comp_id\":\"CA\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}}" }, { "id": "gen-ions-4ins", "prompt": "Load 4INS; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 598 (char 597)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ion\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"spacefill\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}}" }, { "id": "gen-ligands-1cbs", "prompt": "Load 1CBS; show the protein as a grey cartoon and the ligands as purple ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 606 (char 605)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"purple\"}}]}]}]}]}]}}" }, { "id": "gen-ligands-2hhb", "prompt": "Load 2HHB; show the protein as a grey cartoon and the ligands as teal ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 604 (char 603)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"teal\"}}]}]}]}]}]}}" }, { "id": "gen-ligands-3ptb", "prompt": "Load 3PTB; show the protein as a grey cartoon and the ligands as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 606 (char 605)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-range-1cbs", "prompt": "Load 1CBS; protein as grey cartoon, and show residues 20-60 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 660 (char 659)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":20,\"end_auth_seq_id\":60}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-range-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show residues 30-90 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 660 (char 659)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":30,\"end_auth_seq_id\":90}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-range-1lyz", "prompt": "Load 1LYZ; protein as grey cartoon, and show residues 40-80 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 660 (char 659)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":40,\"end_auth_seq_id\":80}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-range-2hhb", "prompt": "Load 2HHB; protein as grey cartoon, and show residues 10-70 of chain B as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 660 (char 659)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\",\"beg_auth_seq_id\":10,\"end_auth_seq_id\":70}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-range-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show residues 50-110 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 661 (char 660)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"beg_auth_seq_id\":50,\"end_auth_seq_id\":110}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-range-4ins", "prompt": "Load 4INS; protein as grey cartoon, and show residues 5-25 of chain B as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 675 (char 674)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"B\",\"beg_auth_seq_id\":5,\"end_auth_seq_id\":25}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "gen-surface-1cbs", "prompt": "Load 1CBS; render the protein as a steelblue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 427 (char 426)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"steelblue\"}}]}]}]}]}]}}" }, { "id": "gen-surface-1lyz", "prompt": "Load 1LYZ; render the protein as a khaki molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 423 (char 422)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1lyz.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"khaki\"}}]}]}]}]}]}}" }, { "id": "gen-surface-2hhb", "prompt": "Load 2HHB; render the protein as a salmon molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 424 (char 423)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"salmon\"}}]}]}]}]}]}}" }, { "id": "gen-surface-3ptb", "prompt": "Load 3PTB; render the protein as a plum molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 422 (char 421)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"plum\"}}]}]}]}]}]}}" }, { "id": "grd-disulfide-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "grd-disulfide-4ins", "prompt": "Load 4INS; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 683 (char 682)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_comp_id\":\"CYS\"},{\"auth_asym_id\":\"B\",\"auth_comp_id\":\"CYS\"}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"yellow\"}}]}]}]}]}]}}" }, { "id": "grd-ligand-1cbs-rea", "prompt": "Load 1CBS; show the protein as a grey cartoon and the REA as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 672 (char 671)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"label_comp_id\":\"REA\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "grd-ligand-1hho-hem", "prompt": "Load 1HHO; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 620 (char 619)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"HEM\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "grd-ligand-2hhb-hem", "prompt": "Load 2HHB; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 620 (char 619)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2hhb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"HEM\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "grd-ligand-3ptb-ca", "prompt": "Load 3PTB; show the protein as a grey cartoon and the CA as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 636 (char 635)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":480}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "grd-ligand-4ins-zn", "prompt": "Load 4INS; show the protein as a grey cartoon and the ZN as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 651 (char 650)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/4ins.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"ZN\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}}" }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 1024 (char 1023)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":64},{\"auth_asym_id\":\"A\",\"auth_seq_id\":157}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"white\"}}]}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":64,\"label_atom_id\":\"NE2\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":157,\"label_atom_id\":\"O2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}} Å\"}}]}]}]}]}}" }, { "id": "int-002", "prompt": "Load 1A6M with the protein as a grey cartoon. Show the heme and the proximal histidine as ball-and-stick and measure the distance from the heme iron to the histidine's coordinating nitrogen.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 995 (char 994)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1a6m.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"label_comp_id\":\"HEM\"},{\"auth_asym_id\":\"A\",\"auth_seq_id\":93}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]},{\"kind\":\"primitives\",\"params\":{\"color\":\"yellow\",\"label_color\":\"yellow\"},\"children\":[{\"kind\":\"primitive\",\"params\":{\"kind\":\"distance_measurement\",\"start\":{\"label_comp_id\":\"HEM\",\"label_atom_id\":\"FE\"},\"end\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":93,\"label_atom_id\":\"NE2\"},\"radius\":0.06,\"dash_length\":0.15,\"label_template\":\"{{distance}} Å\"}}]}]}]}]}}" }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 700 (char 699)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\",\"model_index\":0},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\",\"size_factor\":1.0},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":[{\"auth_asym_id\":\"A\",\"auth_seq_id\":57},{\"auth_asym_id\":\"A\",\"auth_seq_id\":102},{\"auth_asym_id\":\"A\",\"auth_seq_id\":195}]},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\",\"size_factor\":1.0},\"children\":[{\"kind\":\"color" }, { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "int-006", "prompt": "Load haemoglobin 1HHO; show the protein as a 50% transparent surface and the heme groups as ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 668 (char 667)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"surface\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"silver\"}},{\"kind\":\"opacity\",\"params\":{\"opacity\":0.5}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_comp_id\":\"HEM\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]}]}]}" }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 420 (char 419)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/9mxl.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]}]}]}},{\"kind\":\"focus\",\"params\":{\"radius\":20}}]}}" }, { "id": "res-lysozyme", "prompt": "Show me hen egg white lysozyme", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 422 (char 421)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/2vb1.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]}]}]}]}}" }, { "id": "res-myoglobin", "prompt": "Show me sperm whale myoglobin", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 626 (char 625)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/5yce.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"label_comp_id\":\"HEM\"}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]},\"kind\":\"focus\",\"params\":{\"radius\":20}}]}}" }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 422 (char 421)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/7s5h.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]}]}]}]}}" }, { "id": "res-pde5a", "prompt": "I wanna see a structure of PDE5A", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 603 (char 602)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tbf.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":\"ligand\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"orange\"}}]}]}]}]]}]}" } ] }, "qwen/qwen3-30b-a3b-instruct-2507": { "outcomes": { "valid": 22, "unchecked": 0, "invalid_json": 46, "not_mvs": 0, "invalid_mvs": 2, "load_failed": 0 }, "n": 70, "mvs_f1": 0.2659, "failures": [ { "id": "mvs-002", "prompt": "Load haemoglobin (1HHO); show the protein as a grey cartoon and the heme groups as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 16 column 1 (char 1041)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 143}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\", \"auth_seq_id\": 147}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}\n ]}]}]}]}\n]}}" }, { "id": "mvs-004", "prompt": "Load HIV-1 protease (1HVR); protein as grey cartoon, the bound inhibitor as magenta ball-and-stick, and focus the camera on the inhibitor.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 15 column 1 (char 946)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hvr.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 263}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 263}}, \"children\": [\n {\"kind\": \"focus\", \"params\": {\"radius\": 1.5}}]}\n ]}]}]}]}\n]}" }, { "id": "clinvar-1tup-D281", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant D281Y as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 569)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 281}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]\n }\n ]}]}\n ]}\n ]}\n]}}" }, { "id": "clinvar-1tup-N239", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant N239T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 8 column 69 (char 566)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 239}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\", \"size_factor\": 1.0}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}]}" }, { "id": "clinvar-1tup-S215", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S215T as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 8 column 69 (char 566)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 215}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\", \"size_factor\": 1.0}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}]}" }, { "id": "clinvar-1tup-S241", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S241Y as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 8 column 69 (char 546)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 241}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}]}" }, { "id": "hotspots-1tup", "prompt": "In p53 (PDB 1TUP), chain A, highlight the 6 mutational hotspot residues — the positions carrying the most pathogenic ClinVar variants — as red spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 20 column 14 (char 897)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\n \"selector\": [\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 215},\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 109},\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 281},\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 110},\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 239},\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 241}\n ]\n }, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"spacefill\", \"size_factor\": 1.2}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}\n ]}\n ]}\n ]}]}]}]}]}" }, { "id": "named-1tup-143", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 143 and show it as blue ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 8 column 70 (char 547)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 143}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"blue\"}}]}]}]}]}]}]}]}" }, { "id": "named-1tup-248", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 248 and show it as blue ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 8 column 70 (char 547)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1tup.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 248}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"blue\"}}]}]}]}]}]}]}]}" }, { "id": "gen-cartoon-1cbs", "prompt": "Load cellular retinoic-acid binding protein (1CBS) and show the protein as a purple cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 538)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1cbs.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"purple\"}}\n ]}\n ]}\n ]}]}]}\n ]}\n]}" }, { "id": "gen-cartoon-1hho", "prompt": "Load haemoglobin (1HHO) and show the protein as a red cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 8 column 69 (char 507)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]}]}]}]}]}]}" }, { "id": "gen-cartoon-1lyz", "prompt": "Load lysozyme (1LYZ) and show the protein as a green cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 9 column 14 (char 515)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1lyz.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"green\"}}]}]}\n ]}]}]}]}]}" }, { "id": "gen-cartoon-2hhb", "prompt": "Load deoxyhaemoglobin (2HHB) and show the protein as a teal cartoon.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 10 column 1 (char 515)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/2hhb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"teal\"}}]}]}\n ]}]}]}]}\n]}}" }, { "id": "gen-chain-1cbs", "prompt": "Load 1CBS; show everything as a grey cartoon, then colour chain A purple.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 14 (char 869)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1cbs.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}],\n \"custom\": {\"molstar_show_non_covalent_interactions\": true, \"molstar_non_covalent_interactions_radius_ang\": 5}},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"purple\"}}]}]}\n ]}]}]}]}]}" }, { "id": "gen-chain-1lyz", "prompt": "Load 1LYZ; show everything as a grey cartoon, then colour chain A green.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 750)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1lyz.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"green\"}}]}]}\n ]}]}]}]}\n]}}" }, { "id": "gen-focus-1cbs", "prompt": "Load 1CBS; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1cbs.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 200, "label_comp_id": "REA" } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 2.5 } } ] } ] } ] } ] } } }, { "id": "gen-focus-1hho", "prompt": "Load 1HHO; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 25 column 14 (char 1887)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 150}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\", \"auth_seq_id\": 150}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 143}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\", \"auth_seq_id\": 147}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 142}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}]},\n {\"kind\": \"focus\", \"params\": {\"radius\": 1.5}}\n ]}]}]}]}]}" }, { "id": "gen-focus-2hhb", "prompt": "Load 2HHB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 28 column 14 (char 2151)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/2hhb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 142}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\", \"auth_seq_id\": 148}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"C\", \"auth_seq_id\": 142}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"D\", \"auth_seq_id\": 148}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\", \"auth_seq_id\": 147}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"D\", \"auth_seq_id\": 147}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}]},\n {\"kind\": \"focus\", \"params\": {\"radius\": 1.5}}\n ]}]}]}]}]}" }, { "id": "gen-focus-3ptb", "prompt": "Load 3PTB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/3ptb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 1 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 480 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 2.0, "target": { "auth_asym_id": "A", "auth_seq_id": 1 } } }, { "kind": "focus", "params": { "radius": 2.0, "target": { "auth_asym_id": "A", "auth_seq_id": 480 } } } ] } ] } ] } ] } } }, { "id": "gen-ions-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 757)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": \"ion\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"spacefill\", \"size_factor\": 1.2}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"purple\"}}]}]}\n ]}]}]}]}\n]}}" }, { "id": "gen-ions-2hhb", "prompt": "Load 2HHB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 757)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/2hhb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": \"ion\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"spacefill\", \"size_factor\": 1.2}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"purple\"}}]}]}\n ]}]}]}]}\n]}}" }, { "id": "gen-ions-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 757)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": \"ion\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"spacefill\", \"size_factor\": 1.2}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"purple\"}}]}]}\n ]}]}]}]}\n]}}" }, { "id": "gen-ions-4ins", "prompt": "Load 4INS; protein as grey cartoon, and show the ions as purple spheres.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 773)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/4ins.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"type_symbol\": \"ZN\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"spacefill\", \"size_factor\": 1.5}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"purple\"}}]}]}\n ]}]}]}]}\n]}}" }, { "id": "gen-ligands-1cbs", "prompt": "Load 1CBS; show the protein as a grey cartoon and the ligands as purple ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 17 column 1 (char 880)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1cbs.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}],\n \"custom\": {\"molstar_color_theme_name\": \"sequence-id\"}},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 200, \"label_comp_id\": \"REA\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"purple\"}}]}]\n }\n ]}]}\n ]}\n ]}\n]}}" }, { "id": "gen-ligands-2hhb", "prompt": "Load 2HHB; show the protein as a grey cartoon and the ligands as teal ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 34 column 1 (char 2129)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/2hhb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 142}},\n \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"teal\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\", \"auth_seq_id\": 148}},\n \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"teal\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"C\", \"auth_seq_id\": 142}},\n \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"teal\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"D\", \"auth_seq_id\": 148}},\n \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"teal\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\", \"auth_seq_id\": 147}},\n \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"teal\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"D\", \"auth_seq_id\": 147}},\n \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"teal\"}}]}]}\n ]}]}]}]}\n]}}" }, { "id": "gen-range-1cbs", "prompt": "Load 1CBS; protein as grey cartoon, and show residues 20-60 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 806)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1cbs.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": [{\"auth_asym_id\": \"A\", \"beg_auth_seq_id\": 20, \"end_auth_seq_id\": 60}]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}\n ]}]}]}]}\n]}}" }, { "id": "gen-range-1hho", "prompt": "Load 1HHO; protein as grey cartoon, and show residues 30-90 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 806)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": [{\"auth_asym_id\": \"A\", \"beg_auth_seq_id\": 30, \"end_auth_seq_id\": 90}]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}\n ]}]}]}]}\n]}" }, { "id": "gen-range-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and show residues 50-110 of chain A as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 807)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": [{\"auth_asym_id\": \"A\", \"beg_auth_seq_id\": 50, \"end_auth_seq_id\": 110}]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}\n ]}]}]}]}\n]}}" }, { "id": "gen-range-4ins", "prompt": "Load 4INS; protein as grey cartoon, and show residues 5-25 of chain B as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 803)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/4ins.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\", \"beg_auth_seq_id\": 5, \"end_auth_seq_id\": 25}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}\n ]}]}]}]}\n]}" }, { "id": "gen-surface-1cbs", "prompt": "Load 1CBS; render the protein as a steelblue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 12 column 4 (char 536)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1cbs.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"surface\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"steelblue\"}}\n ]}\n ]}\n ]}]\n ]}\n]}}]}" }, { "id": "gen-surface-1hho", "prompt": "Load 1HHO; render the protein as a steelblue molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 8 column 75 (char 513)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"surface\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"steelblue\"}}]}]}]}]}]}]}]}" }, { "id": "gen-surface-3ptb", "prompt": "Load 3PTB; render the protein as a plum molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 14 column 1 (char 561)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"surface\", \"size_factor\": 1.0}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"plum\"}}\n ]}\n ]}\n ]}]}\n ]}\n ]}\n]}}" }, { "id": "gen-surface-4ins", "prompt": "Load 4INS; render the protein as a salmon molecular surface.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 12 column 1 (char 535)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/4ins.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"surface\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"salmon\"}}\n ]}\n ]}\n ]}]}]}]}\n]}}" }, { "id": "grd-disulfide-3ptb", "prompt": "Load 3PTB; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 15 column 1 (char 830)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": [{\"auth_asym_id\": \"A\", \"auth_seq_id\": 18}, {\"auth_asym_id\": \"A\", \"auth_seq_id\": 171}]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"yellow\"}}]}]}\n ]}]}\n ]}\n ]}\n]}}" }, { "id": "grd-disulfide-4ins", "prompt": "Load 4INS; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 16 column 1 (char 1217)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/4ins.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": [{\"auth_asym_id\": \"A\", \"auth_seq_id\": 7, \"label_atom_id\": \"SG\"}, {\"auth_asym_id\": \"B\", \"auth_seq_id\": 7, \"label_atom_id\": \"SG\"}]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"yellow\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": [{\"auth_asym_id\": \"A\", \"auth_seq_id\": 19, \"label_atom_id\": \"SG\"}, {\"auth_asym_id\": \"B\", \"auth_seq_id\": 19, \"label_atom_id\": \"SG\"}]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"yellow\"}}]}]}\n ]}]}]}]}\n]}}" }, { "id": "grd-ligand-1cbs-rea", "prompt": "Load 1CBS; show the protein as a grey cartoon and the REA as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 802)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1cbs.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 200, \"label_comp_id\": \"REA\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}\n ]}]}]}]}\n]}}" }, { "id": "grd-ligand-2hhb-hem", "prompt": "Load 2HHB; show the protein as a grey cartoon and the HEM as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 12 column 14 (char 759)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/2hhb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_comp_id\": \"HEM\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}\n ]}]}]}]}]}" }, { "id": "grd-ligand-3ptb-ca", "prompt": "Load 3PTB; show the protein as a grey cartoon and the CA as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 781)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_atom_id\": \"CA\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}\n ]}]}]}]}\n]}" }, { "id": "grd-ligand-4ins-zn", "prompt": "Load 4INS; show the protein as a grey cartoon and the ZN as orange ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 13 column 1 (char 759)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/4ins.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_comp_id\": \"ZN\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}\n ]}]}]}]}\n]}}" }, { "id": "int-001", "prompt": "In oxymyoglobin 1A6M, show the protein as a grey cartoon, His64 and the bound O2 as ball-and-stick, and draw the hydrogen bond from His64 NE2 to the O2 molecule's terminal oxygen (atom O2) as a dashed line labelled with its length.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 22 column 14 (char 1548)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1a6m.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 64, \"label_comp_id\": \"HIS\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 157, \"label_comp_id\": \"OXY\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]},\n {\"kind\": \"primitives\", \"params\": {\"color\": \"blue\", \"label_color\": \"blue\", \"opacity\": 0.8}, \"children\": [\n {\"kind\": \"primitive\", \"params\": {\"kind\": \"distance_measurement\",\n \"start\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 64, \"label_atom_id\": \"NE2\"},\n \"end\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 157, \"label_atom_id\": \"O2\"},\n \"radius\": 0.06,\n \"dash_length\": 0.15,\n \"label_template\": \"{{distance}}\"}}]}\n ]}]}]}]}]}]}" }, { "id": "int-002", "prompt": "Load 1A6M with the protein as a grey cartoon. Show the heme and the proximal histidine as ball-and-stick and measure the distance from the heme iron to the histidine's coordinating nitrogen.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 22 column 14 (char 1533)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1a6m.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"HEM\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 154, \"label_atom_id\": \"NA\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]},\n {\"kind\": \"primitives\", \"params\": {\"color\": \"blue\", \"label_color\": \"blue\", \"opacity\": 0.7}, \"children\": [\n {\"kind\": \"primitive\", \"params\": {\"kind\": \"distance_measurement\",\n \"start\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"HEM\", \"label_atom_id\": \"FE\"},\n \"end\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 154, \"label_atom_id\": \"NA\"},\n \"radius\": 0.05,\n \"dash_length\": 0.1,\n \"label_template\": \"{{distance}} Å\"}}]}\n ]}]}]}]}]}]}" }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 31 column 14 (char 2289)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"grey\"}}]}],\n \"custom\": {\"molstar_show_non_covalent_interactions\": true, \"molstar_non_covalent_interactions_radius_ang\": 5}},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 57, \"label_comp_id\": \"HIS\"}},\n \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 102, \"label_comp_id\": \"ASP\"}},\n \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 195, \"label_comp_id\": \"SER\"}},\n \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]},\n {\"kind\": \"primitives\", \"params\": {\"color\": \"blue\", \"label_color\": \"blue\", \"opacity\": 0.7}, \"children\": [\n {\"kind\": \"primitive\", \"params\": {\"kind\": \"distance_measurement\",\n \"start\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 57, \"label_atom_id\": \"ND1\"},\n \"end\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 102, \"label_atom_id\": \"OD1\"},\n \"radius\": 0.05, \"dash_length\": 0.1, \"label_template\": \"{{distance}}\" }},\n {\"kind\": \"primitive\", \"params\": {\"kind\": \"distance_measurement\",\n \"start\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 102, \"label_atom_id\": \"OD2\"},\n \"end\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 195, \"label_atom_id\": \"OG\"},\n \"radius\": 0.05, \"dash_length\": 0.1, \"label_template\": \"{{distance}}\" }}]}\n ]}]}]}]}]}" }, { "id": "int-004", "prompt": "Load 1A6M with the protein as a grey cartoon and show all the non-covalent interactions (hydrogen bonds, metal contacts) around the bound oxygen molecule.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 15 column 1 (char 1037)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1a6m.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}],\n \"custom\": {\"molstar_show_non_covalent_interactions\": true, \"molstar_non_covalent_interactions_radius_ang\": 5}},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 157, \"label_comp_id\": \"OXY\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}],\n \"custom\": {\"molstar_show_non_covalent_interactions\": true, \"molstar_non_covalent_interactions_radius_ang\": 5}}\n ]}]}]}]}\n]}" }, { "id": "int-005", "prompt": "Show trypsin 3PTB as a grey cartoon and display the interactions between the benzamidine inhibitor and the protein.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 26 column 14 (char 2101)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 1, \"label_comp_id\": \"BEN\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"blue\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 480, \"label_comp_id\": \"CA\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": \"water\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"lightblue\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 1, \"label_comp_id\": \"BEN\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 1, \"label_comp_id\": \"BEN\"}}, \"children\": [\n {\"kind\": \"custom\", \"params\": {\"molstar_show_non_covalent_interactions\": true, \"molstar_non_covalent_interactions_radius_ang\": 5}}]}\n ]}]}]}]}]}" }, { "id": "int-006", "prompt": "Load haemoglobin 1HHO; show the protein as a 50% transparent surface and the heme groups as ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 23 column 4 (char 1172)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1hho.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"surface\", \"size_factor\": 1.0}, \"children\": [\n {\"kind\": \"opacity\", \"params\": {\"opacity\": 0.5}},\n {\"kind\": \"color\", \"params\": {\"color\": \"steelblue\"}}\n ]}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 143}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}\n ]}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\", \"auth_seq_id\": 147}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}\n ]}\n ]}\n ]}]\n ]}\n]}}" }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 22 column 1 (char 1255)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/9MXL.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"steelblue\", \"custom\": {\"molstar_color_theme_name\": \"sequence-id\"}}}\n ]},\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\", \"size_factor\": 0.5}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\", \"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"CL\"}}}\n ]}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\", \"size_factor\": 0.5}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}\n ]}\n ]},\n {\"kind\": \"label\", \"params\": {\"text\": \"CFTR (P13569)\", \"position\": [0, 0, 0], \"label_size\": 0.5}},\n {\"kind\": \"focus\", \"params\": {\"radius\": 5.0}}\n ]}]}]}]}\n]}}" }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 30 column 1 (char 1475)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/7S5H.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\", \"size_factor\": 1.0}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"blue\"}}\n ]}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 1}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\", \"size_factor\": 1.2}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}\n ]}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"B\", \"auth_seq_id\": 1}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\", \"size_factor\": 1.2}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}\n ]}\n ]},\n {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\", \"size_factor\": 1.2}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}\n ]}\n ]},\n {\"kind\": \"focus\", \"params\": {\"radius\": 5.0}}\n ]}]}\n ]}\n ]}\n]}}" }, { "id": "res-pde5a", "prompt": "I wanna see a structure of PDE5A", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 78 column 99 (char 6759)", "raw": "{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1TBF.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"steelblue\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"FE2\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"red\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D8E\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"H8B\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"green\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D13\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"purple\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D14\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"cyan\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D15\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"magenta\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D16\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"brown\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D17\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"pink\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D18\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"lime\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D19\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gold\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D20\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"indigo\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D21\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"teal\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D22\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"crimson\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D23\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"salmon\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D24\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"olive\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D25\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"navy\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D26\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"maroon\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D27\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"darkgreen\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D28\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"darkblue\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D29\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"darkred\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D30\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"darkorange\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D31\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"darkviolet\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D32\"}}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"darkkhaki\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"D33\"}}, \"children\": [\n" } ] }, "qwen/qwen3-next-80b-a3b-instruct": { "outcomes": { "valid": 64, "unchecked": 0, "invalid_json": 0, "not_mvs": 0, "invalid_mvs": 6, "load_failed": 0 }, "n": 70, "mvs_f1": 0.8303, "failures": [ { "id": "mvs-004", "prompt": "Load HIV-1 protease (1HVR); protein as grey cartoon, the bound inhibitor as magenta ball-and-stick, and focus the camera on the inhibitor.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1hvr.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 263 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 } } ] } ] } ] } ] } } }, { "id": "named-1tup-175", "prompt": "In p53 (PDB 1TUP), chain A, select the residue at canonical UniProt position 175 and show it as blue ball-and-stick.", "outcome": "invalid_mvs", "mvs_issues": [ "Invalid parameters for node of kind \"component\":", " Missing required parameter \"selector\"." ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1tup.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "auth_asym_id": "A", "auth_seq_id": 175 }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "blue" } } ] } ] } ] } ] } ] } ] } } }, { "id": "gen-focus-1cbs", "prompt": "Load 1CBS; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1cbs.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_seq_id": 200 } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 } } ] } ] } ] } ] } } }, { "id": "gen-focus-1hho", "prompt": "Load 1HHO; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/1hho.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": {} } ] } ] } ] } ] } } }, { "id": "gen-focus-2hhb", "prompt": "Load 2HHB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/2hhb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 } } ] } ] } ] } ] } } }, { "id": "gen-focus-3ptb", "prompt": "Load 3PTB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/3ptb.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "polymer" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "gray" } } ] } ] }, { "kind": "component", "params": { "selector": { "auth_asym_id": "A", "auth_comp_id": "BEN" } }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "magenta" } } ] } ] }, { "kind": "focus", "params": { "radius": 5 } } ] } ] } ] } ] } } } ] }, "z-ai/glm-5.2": { "outcomes": { "valid": 60, "unchecked": 0, "invalid_json": 8, "not_mvs": 0, "invalid_mvs": 2, "load_failed": 0 }, "n": 70, "mvs_f1": 0.7832, "failures": [ { "id": "clinvar-1tup-S241", "prompt": "In p53 (PDB 1TUP), chain A, highlight the residue affected by the pathogenic ClinVar variant S241Y as red ball-and-stick.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 650 (char 649)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1tup.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"auth_asym_id\":\"A\",\"auth_seq_id\":241}},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"red\"}}]},{\"kind\":\"focus\"}]}]}]}]}}]}" }, { "id": "gen-chain-1cbs", "prompt": "Load 1CBS; show everything as a grey cartoon, then colour chain A purple.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 488 (char 487)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1cbs.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}},{\"kind\":\"color\",\"params\":{\"color\":\"purple\",\"selector\":{\"auth_asym_id\":\"A\"}}]}]}]}]}]}]}}" }, { "id": "gen-chain-1hho", "prompt": "Load 1HHO; show everything as a grey cartoon, then colour chain A red.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 485 (char 484)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/1hho.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"polymer\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}},{\"kind\":\"color\",\"params\":{\"color\":\"red\",\"selector\":{\"auth_asym_id\":\"A\"}}]}]}]}]}]}]}}" }, { "id": "gen-focus-3ptb", "prompt": "Load 3PTB; grey cartoon protein, magenta ball-and-stick ligands, and focus the camera on the ligand.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 1 column 644 (char 643)", "raw": "{\"root\":{\"kind\":\"root\",\"children\":[{\"kind\":\"download\",\"params\":{\"url\":\"https://files.rcsb.org/download/3ptb.cif\"},\"children\":[{\"kind\":\"parse\",\"params\":{\"format\":\"mmcif\"},\"children\":[{\"kind\":\"structure\",\"params\":{\"type\":\"model\"},\"children\":[{\"kind\":\"component\",\"params\":{\"selector\":\"protein\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"cartoon\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"gray\"}}]}]},{\"kind\":\"component\",\"params\":{\"selector\":{\"label_comp_id\":\"BEN\"},\"children\":[{\"kind\":\"representation\",\"params\":{\"type\":\"ball_and_stick\"},\"children\":[{\"kind\":\"color\",\"params\":{\"color\":\"magenta\"}}]},{\"kind\":\"focus\",\"params\":{}}]}]}]}]}]}}" }, { "id": "grd-disulfide-4ins", "prompt": "Load 4INS; protein as grey cartoon, and highlight the disulfide-bonded cysteines as yellow ball-and-stick.", "outcome": "invalid_json", "error": "no JSON object found in output", "raw": "" }, { "id": "int-003", "prompt": "In trypsin (3PTB), show the protein as a grey cartoon and the catalytic triad (His57, Asp102, Ser195) as ball-and-stick. Draw the two triad hydrogen bonds as dashed lines with their lengths.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 20 column 83 (char 1319)", "raw": "```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/3ptb.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"protein\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": [\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 57},\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 102},\n {\"auth_asym_id\": \"A\", \"auth_seq_id\": 195}\n ]}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"lightgreen\"}}]}]},\n {\"kind\": \"primitives\", \"params\": {\"color\": \"yellow\", \"label_color\": \"yellow\"}, \"children\": [\n {\"kind\": \"primitive\", \"params\": {\"kind\": \"distance_measurement\",\n \"start\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 57, \"label_atom_id\": \"ND1\"},\n \"end\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 102, \"label_atom_id\": \"OD1\"},\n \"radius\": 0.06, \"dash_length\": 0.15, \"label_template\": \"{{distance}}\"}}},\n {\"kind\": \"primitive\", \"params\": {\"kind\": \"distance_measurement\",\n \"start\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 195, \"label_atom_id\": \"OG\"},\n \"end\": {\"auth_asym_id\": \"A\", \"auth_seq_id\": 57, \"label_atom_id\": \"NE2\"},\n \"radius\": 0.06, \"dash_length\": 0.15, \"label_template\": \"{{distance}}\"}}]}\n ]}]}]}\n]}}\n```" }, { "id": "int-004", "prompt": "Load 1A6M with the protein as a grey cartoon and show all the non-covalent interactions (hydrogen bonds, metal contacts) around the bound oxygen molecule.", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 10 column 6 (char 733)", "raw": "```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/1a6m.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"gray\"}}]}]},\n {\"kind\": \"component\", \"params\": {\"selector\": {\"auth_asym_id\": \"A\", \"label_comp_id\": \"OXY\"}, \"custom\": {\"molstar_show_non_covalent_interactions\": true, \"molstar_non_covalent_interactions_radius_ang\": 5}, \"children\": []}\n ]}]}]}\n]}}\n```" }, { "id": "res-cftr", "prompt": "show me the CFTR channel", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/9MXL.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue", "custom": { "molstar_color_theme_name": "secondary-structure" } } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "component", "params": { "selector": "ion" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "purple" } } ] } ] }, { "kind": "focus", "params": { "radius": 10 } } ] } ] } ] } ] } } }, { "id": "res-lysozyme", "prompt": "Show me hen egg white lysozyme", "outcome": "invalid_mvs", "mvs_issues": [ "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_representation\"" ], "predicted": { "root": { "kind": "root", "children": [ { "kind": "download", "params": { "url": "https://files.rcsb.org/download/2vb1.cif" }, "children": [ { "kind": "parse", "params": { "format": "mmcif" }, "children": [ { "kind": "structure", "params": { "type": "model" }, "children": [ { "kind": "component", "params": { "selector": "protein" }, "children": [ { "kind": "representation", "params": { "type": "cartoon" }, "children": [ { "kind": "color", "params": { "color": "steelblue" } } ] } ] }, { "kind": "component", "params": { "selector": "ligand" }, "children": [ { "kind": "representation", "params": { "type": "ball_and_stick" }, "children": [ { "kind": "color", "params": { "color": "orange" } } ] } ] }, { "kind": "focus" } ] } ] } ] } ] } } }, { "id": "res-pcsk9", "prompt": "show the structure of PCSK9", "outcome": "invalid_json", "error": "JSON parse error: Expecting ',' delimiter: line 14 column 3 (char 841)", "raw": "```json\n{\"root\": {\"kind\": \"root\", \"children\": [\n {\"kind\": \"download\", \"params\": {\"url\": \"https://files.rcsb.org/download/7s5h.cif\"},\n \"children\": [\n {\"kind\": \"parse\", \"params\": {\"format\": \"mmcif\"}, \"children\": [\n {\"kind\": \"structure\", \"params\": {\"type\": \"model\"}, \"children\": [\n {\"kind\": \"component\", \"params\": {\"selector\": \"polymer\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"cartoon\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"steelblue\"}, \"custom\": {\"molstar_color_theme_name\": \"secondary-structure\"}},\n {\"kind\": \"focus\"}]},\n {\"kind\": \"component\", \"params\": {\"selector\": \"ligand\"}, \"children\": [\n {\"kind\": \"representation\", \"params\": {\"type\": \"ball_and_stick\"}, \"children\": [\n {\"kind\": \"color\", \"params\": {\"color\": \"orange\"}}]}]}\n ]}]}]}\n]}}}\n```" } ] } }, "bare": { "claude-haiku-4-5": { "outcomes": { "valid": 0, "unchecked": 0, "invalid_json": 0, "not_mvs": 0, "invalid_mvs": 70, "load_failed": 0 }, "n": 70, "mvs_f1": 0.0 }, "deepseek/deepseek-v3.2": { "outcomes": { "valid": 0, "unchecked": 0, "invalid_json": 0, "not_mvs": 0, "invalid_mvs": 70, "load_failed": 0 }, "n": 70, "mvs_f1": 0.0 }, "qwen/qwen3-30b-a3b-instruct-2507": { "outcomes": { "valid": 0, "unchecked": 0, "invalid_json": 15, "not_mvs": 0, "invalid_mvs": 55, "load_failed": 0 }, "n": 70, "mvs_f1": 0.0 } }, "bare_grounded": { "claude-haiku-4-5": { "outcomes": { "valid": 0, "unchecked": 0, "invalid_json": 2, "not_mvs": 0, "invalid_mvs": 68, "load_failed": 0 }, "n": 70, "mvs_f1": 0.0 }, "deepseek/deepseek-v3.2": { "outcomes": { "valid": 0, "unchecked": 0, "invalid_json": 0, "not_mvs": 0, "invalid_mvs": 70, "load_failed": 0 }, "n": 70, "mvs_f1": 0.0 }, "qwen/qwen3-30b-a3b-instruct-2507": { "outcomes": { "valid": 0, "unchecked": 0, "invalid_json": 8, "not_mvs": 0, "invalid_mvs": 62, "load_failed": 0 }, "n": 70, "mvs_f1": 0.0 } } }, "mvs_messages": [ { "pattern": "Invalid parameters for node of kind \"…\": Missing required parameter \"…\".", "counts": { "spec": 1, "spec_grounded": 2, "bare": 195, "bare_grounded": 199 }, "total": 397, "n_models": 5, "examples": [ { "text": "Invalid parameters for node of kind \"download\": Missing required parameter \"url\".", "n": 377 }, { "text": "Invalid parameters for node of kind \"structure\": Missing required parameter \"type\".", "n": 9 }, { "text": "Invalid parameters for node of kind \"component\": Missing required parameter \"selector\".", "n": 6 }, { "text": "Invalid parameters for node of kind \"parse\": Missing required parameter \"format\".", "n": 4 }, { "text": "Invalid parameters for node of kind \"representation\": Missing required parameter \"type\".", "n": 1 } ] }, { "pattern": "Node of kind \"…\" cannot appear as a child of \"…\". Allowed parents: …", "counts": { "spec": 28, "spec_grounded": 43 }, "total": 71, "n_models": 12, "examples": [ { "text": "Node of kind \"focus\" cannot appear as a child of \"structure\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_re…", "n": 63 }, { "text": "Node of kind \"component\" cannot appear as a child of \"component\". Allowed parents for \"component\" are: \"structure\"", "n": 2 }, { "text": "Node of kind \"focus\" cannot appear as a child of \"representation\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volu…", "n": 2 }, { "text": "Node of kind \"focus\" cannot appear as a child of \"color\". Allowed parents for \"focus\" are: \"root\", \"component\", \"component_from_uri\", \"component_from_source\", \"primitives\", \"primitives_from_uri\", \"volume\", \"volume_repres…", "n": 2 }, { "text": "Node of kind \"color\" cannot appear as a child of \"component\". Allowed parents for \"color\" are: \"representation\", \"volume_representation\"", "n": 1 }, { "text": "Node of kind \"representation\" cannot appear as a child of \"structure\". Allowed parents for \"representation\" are: \"component\", \"component_from_uri\", \"component_from_source\"", "n": 1 } ] }, { "pattern": "Invalid parameters for node of kind \"…\": Invalid value for parameter \"…\":", "counts": { "spec": 5, "spec_grounded": 6, "bare_grounded": 1 }, "total": 12, "n_models": 5, "examples": [ { "text": "Invalid parameters for node of kind \"representation\": Invalid value for parameter \"type\":", "n": 6 }, { "text": "Invalid parameters for node of kind \"component\": Invalid value for parameter \"selector\":", "n": 5 }, { "text": "Invalid parameters for node of kind \"color\": Invalid value for parameter \"color\":", "n": 1 } ] }, { "pattern": "Unknown node kind \"…\"", "counts": { "spec": 2, "spec_grounded": 1 }, "total": 3, "n_models": 1, "examples": [ { "text": "Unknown node kind \"custom\"", "n": 3 } ] } ], "json_errors": [ { "pattern": "JSON parse error: Expecting ',' delimiter", "counts": { "spec": 198, "spec_grounded": 218, "bare": 8, "bare_grounded": 6 }, "total": 430 }, { "pattern": "no JSON object found in output", "counts": { "spec": 15, "spec_grounded": 27 }, "total": 42 }, { "pattern": "JSON parse error: Extra data", "counts": { "spec": 13, "spec_grounded": 12, "bare": 7, "bare_grounded": 3 }, "total": 35 }, { "pattern": "JSON parse error: Expecting property name enclosed in double quotes", "counts": { "spec": 1, "spec_grounded": 1, "bare_grounded": 1 }, "total": 3 }, { "pattern": "JSON parse error: Expecting value", "counts": { "spec_grounded": 1 }, "total": 1 } ] }