id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16659 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.3-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""645c2d2f9e69a025b0a37e29"", ""factorPackIds"" : { }, ""deploymentId"" : 240000003 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/erikookamoto/Downloads/fold_250117_ifx_fab_tnfa_monomer/fold_250117_ifx_fab_tnfa_monomer_model_0.cif Chain information for fold_250117_ifx_fab_tnfa_monomer_model_0.cif #1 --- Chain | Description A | . B | . C | . Computing secondary structure > select /A:1-157 1226 atoms, 1253 bonds, 157 residues, 1 model selected > select /A:1-157 1226 atoms, 1253 bonds, 157 residues, 1 model selected Alignment identifier is 1/A > color sel yellow > save ""/Users/erikookamoto/OneDrive - keio.jp/IFX Fab_TNFa monomer.cxs"" > save /Users/erikookamoto/Desktop/image1.png supersample 3 > close session > open > /Users/erikookamoto/Downloads/fold_250117_ada_fab_tnfa_monomer/fold_250117_ada_fab_tnfa_monomer_model_0.cif Chain information for fold_250117_ada_fab_tnfa_monomer_model_0.cif #1 --- Chain | Description A | . B | . C | . Computing secondary structure > select /A:1-214 1647 atoms, 1681 bonds, 214 residues, 1 model selected > select /B:1-218 1631 atoms, 1670 bonds, 218 residues, 1 model selected > select /C:1-157 1226 atoms, 1253 bonds, 157 residues, 1 model selected > color sel yellow > ui windowfill toggle > save /Users/erikookamoto/Desktop/image2.png supersample 3 > open > /Users/erikookamoto/Downloads/fold_250117_glm_fv_tnfa_monomer/fold_250117_glm_fv_tnfa_monomer_model_0.cif Chain information for fold_250117_glm_fv_tnfa_monomer_model_0.cif #2 --- Chain | Description A | . B | . C | . Computing secondary structure > undo > redo > undo > select add #2 3143 atoms, 3217 bonds, 405 residues, 1 model selected > close #2 Alignment identifier is 1/A Alignment identifier is 1/B Alignment identifier is 1/C > select /C:156-157 14 atoms, 13 bonds, 2 residues, 1 model selected > select /C 1226 atoms, 1253 bonds, 157 residues, 1 model selected > color sel yellow > save ""/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/ADA Fab_TNFa > monomer.cxs"" > close session > open > /Users/erikookamoto/Downloads/fold_250117_glm_fv_tnfa_monomer/fold_250117_glm_fv_tnfa_monomer_model_0.cif Chain information for fold_250117_glm_fv_tnfa_monomer_model_0.cif #1 --- Chain | Description A | . B | . C | . Computing secondary structure Alignment identifier is 1/A Alignment identifier is 1/B Alignment identifier is 1/C > select /A:157 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A 1226 atoms, 1253 bonds, 157 residues, 1 model selected > color sel yellow > save /Users/erikookamoto/Desktop/image3.png supersample 3 Unsupported scale factor (0.000000) detected on Display0 > save ""/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/GLM Fv_TNFa > monomer.cxs"" > select > /B:6-10,13-15,21-28,37-42,48-54,61-63,71-76,81-86,95-102,105-107,110-112,116-119,123-127 554 atoms, 556 bonds, 67 residues, 1 model selected Unsupported scale factor (0.000000) detected on Display0 > open > /Users/erikookamoto/Downloads/fold_trastuzumab_her2_extracellular/fold_trastuzumab_her2_extracellular_model_0.cif Chain information for fold_trastuzumab_her2_extracellular_model_0.cif #2 --- Chain | Description A | . B | . C | . Computing secondary structure > undo > select add #2 8139 atoms, 8335 bonds, 1064 residues, 1 model selected > close #2 > close session > open > /Users/erikookamoto/Downloads/fold_trastuzumab_her2_extracellular/fold_trastuzumab_her2_extracellular_model_0.cif Chain information for fold_trastuzumab_her2_extracellular_model_0.cif #1 --- Chain | Description A | . B | . C | . Computing secondary structure Alignment identifier is 1/A Alignment identifier is 1/B Alignment identifier is 1/C > select /A:1 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A 4839 atoms, 4956 bonds, 630 residues, 1 model selected > color sel yellow > save ""/Users/erikookamoto/Library/CloudStorage/OneDrive- > keio.jp/Trastuzumab_HER2 extracellular.cxs"" > save /Users/erikookamoto/Desktop/image4.png supersample 3 > close session > open > /Users/erikookamoto/Downloads/fold_250120_rtx_fab_cd20_extracellular/fold_250120_rtx_fab_cd20_extracellular_model_0.cif Chain information for fold_250120_rtx_fab_cd20_extracellular_model_0.cif #1 --- Chain | Description A | . B | . C | . Computing secondary structure Alignment identifier is 1/A Alignment identifier is 1/B Alignment identifier is 1/C > select /C:47 7 atoms, 6 bonds, 1 residue, 1 model selected > select /C:15-47 265 atoms, 273 bonds, 33 residues, 1 model selected > select /C 384 atoms, 395 bonds, 47 residues, 1 model selected > color sel yellow > save ""/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/RTX > Fab_CD20.cxs"" > save /Users/erikookamoto/Desktop/image5.png supersample 3 > close session > open > /Users/erikookamoto/Downloads/fold_250120_tcz_fab_il6/fold_250120_tcz_fab_il6_model_0.cif Chain information for fold_250120_tcz_fab_il6_model_0.cif #1 --- Chain | Description A | . B | . C | . Computing secondary structure Alignment identifier is 1/A Alignment identifier is 1/B Alignment identifier is 1/C > select /A:346 8 atoms, 8 bonds, 1 residue, 1 model selected > select /A:5-346 2681 atoms, 2758 bonds, 342 residues, 1 model selected > color sel yellow > save /Users/erikookamoto/Desktop/image6.png supersample 3 > save /Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/TCZ_IL-6.cxs Unsupported scale factor (0.000000) detected on Display0 > open ""/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/RTX > Fab_CD20.cxs"" opened ChimeraX session Could not find virtual screen for QCocoaScreen(0x600003cfb230, ""Apple TV (AirPlay)"", QRect(0,0 1920x1080), dpr=1, displayId=75, ) with displayId 75 Unsupported scale factor (0.000000) detected on Display0 > ui tool show Distances > select sel @ show sel target ab > style sel ball Changed 437 atom styles > label sel attribute label_one_letter_code > ui tool show ""Selection Inspector"" > ui tool show ""Show Sequence Viewer"" > sequence chain /A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > select /A:106@CH2 1 atom, 1 residue, 1 model selected > select add /C:30@CB 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance /A:106@CH2 /C:30@CB Distance between /A TRP 106 CH2 and /C ASN 30 CB: 4.352Å > close session > open ""/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/IFX Fab_TNFa > monomer.cxs"" opened ChimeraX session > toolshed show > ui tool show ""Modeller Comparative"" > ui tool show Matchmaker > open 4g3y fromDatabase pdb format mmcif Summary of feedback from opening 4g3y fetched from pdb --- note | Fetching compressed mmCIF 4g3y from http://files.rcsb.org/download/4g3y.cif 4g3y title: Crystal structure of TNF-alpha in complex with Infliximab Fab fragment [more info...] Chain information for 4g3y #2 --- Chain | Description | UniProt C | Tumor necrosis factor | TNFA_HUMAN 1-157 H | infliximab Fab H | L | infliximab Fab L | 4g3y mmCIF Assemblies --- 1| author_defined_assembly 2| software_defined_assembly > ui tool show Matchmaker > matchmaker #2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_250117_ifx_fab_tnfa_monomer_model_0.cif, chain B (#1) with 4g3y, chain H (#2), sequence alignment score = 1113.8 RMSD between 216 pruned atom pairs is 0.564 angstroms; (across all 220 pairs: 0.775) > save /Users/erikookamoto/Desktop/image7.png supersample 3 > close session > open ""/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/ADA Fab_TNFa > monomer.cxs"" opened ChimeraX session > open 3wd5 fromDatabase pdb format mmcif Summary of feedback from opening 3wd5 fetched from pdb --- note | Fetching compressed mmCIF 3wd5 from http://files.rcsb.org/download/3wd5.cif 3wd5 title: Crystal structure of TNFalpha in complex with Adalimumab Fab fragment [more info...] Chain information for 3wd5 #2 --- Chain | Description | UniProt A | Tumor necrosis factor | TNFA_HUMAN 1-157 H | Adalimumab Heavy Chain | L | Adalimumab Light Chain | > ui tool show Matchmaker > matchmaker #!2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_250117_ada_fab_tnfa_monomer_model_0.cif, chain B (#1) with 3wd5, chain H (#2), sequence alignment score = 1066.4 RMSD between 212 pruned atom pairs is 0.854 angstroms; (across all 213 pairs: 0.892) > view > save /Users/erikookamoto/Desktop/image8.png supersample 3 > close session > open ""/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/GLM Fv_TNFa > monomer.cxs"" opened ChimeraX session > open 5yoy fromDatabase pdb format mmcif Summary of feedback from opening 5yoy fetched from pdb --- note | Fetching compressed mmCIF 5yoy from http://files.rcsb.org/download/5yoy.cif 5yoy title: Crystal structure of the human tumor necrosis factor in complex with golimumab Fv [more info...] Chain information for 5yoy #2 --- Chain | Description | UniProt A B C J K L | Tumor necrosis factor | TNFA_HUMAN 1-157 D E F M N O | Golimumab light chain variable region | G H I P Q R | Golimumab heavy chain variable region | 5yoy mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > open 5y0y fromDatabase pdb format mmcif Summary of feedback from opening 5y0y fetched from pdb --- notes | Fetching compressed mmCIF 5y0y from http://files.rcsb.org/download/5y0y.cif Fetching CCD AU from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/AU/AU.cif 5y0y title: RVFV GN-Au [more info...] Chain information for 5y0y #3 --- Chain | Description | UniProt A | NSmGnGc | H9BSP3_RVFV 1-316 Non-standard residues in 5y0y #3 --- AU — gold ion > open 5YOY fromDatabase pdb format mmcif 5yoy title: Crystal structure of the human tumor necrosis factor in complex with golimumab Fv [more info...] Chain information for 5yoy #4 --- Chain | Description | UniProt A B C J K L | Tumor necrosis factor | TNFA_HUMAN 1-157 D E F M N O | Golimumab light chain variable region | G H I P Q R | Golimumab heavy chain variable region | 5yoy mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > open 5yoy fromDatabase pdb format mmcif 5yoy title: Crystal structure of the human tumor necrosis factor in complex with golimumab Fv [more info...] Chain information for 5yoy #5 --- Chain | Description | UniProt A B C J K L | Tumor necrosis factor | TNFA_HUMAN 1-157 D E F M N O | Golimumab light chain variable region | G H I P Q R | Golimumab heavy chain variable region | 5yoy mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > ui tool show ""Color Actions"" > ui tool show Matchmaker > matchmaker #2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_250117_glm_fv_tnfa_monomer_model_0.cif, chain A (#1) with 5yoy, chain A (#2), sequence alignment score = 784.8 RMSD between 145 pruned atom pairs is 0.761 angstroms; (across all 152 pairs: 1.296) > color sel byhetero > color sel bychain > color sel bypolymer > surface hidePatches sel > select > #1/B:6-10,13-15,21-28,37-42,48-54,61-63,71-76,81-86,95-102,105-107,110-112,116-119,123-127 554 atoms, 556 bonds, 67 residues, 1 model selected > style sel sphere Changed 554 atom styles > style sel sphere Changed 554 atom styles > color sel bypolymer > surface hidePatches sel No Surface models open > cartoon sel > view > hide #5 models > close #5 > close #4 > close #3 > close #2 > color sel bynucleotide > view > select /A:118 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:76-118 339 atoms, 347 bonds, 43 residues, 1 model selected > select /A:157 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A 1226 atoms, 1253 bonds, 157 residues, 1 model selected > select > /B:6-10,13-15,21-28,37-42,48-54,61-63,71-76,81-86,95-102,105-107,110-112,116-119,123-127 554 atoms, 556 bonds, 67 residues, 1 model selected > select /C:7-10,13-16,22-28,36-41,48-51,65-70,73-78,88-93,107-110 372 atoms, 370 bonds, 47 residues, 1 model selected > open 5yoy fromDatabase pdb format mmcif 5yoy title: Crystal structure of the human tumor necrosis factor in complex with golimumab Fv [more info...] Chain information for 5yoy #2 --- Chain | Description | UniProt A B C J K L | Tumor necrosis factor | TNFA_HUMAN 1-157 D E F M N O | Golimumab light chain variable region | G H I P Q R | Golimumab heavy chain variable region | 5yoy mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > ui tool show Matchmaker > matchmaker #2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_250117_glm_fv_tnfa_monomer_model_0.cif, chain A (#1) with 5yoy, chain A (#2), sequence alignment score = 784.8 RMSD between 145 pruned atom pairs is 0.761 angstroms; (across all 152 pairs: 1.296) > close session > open ""/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/ADA Fab_TNFa > monomer.cxs"" opened ChimeraX session > view > ui tool show H-Bonds > hbonds saltOnly true reveal true 34 hydrogen bonds found Unsupported scale factor (0.000000) detected on Display0 > close session > open ""/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/RTX > Fab_CD20.cxs"" format session opened ChimeraX session > ui tool show Distances > select /C:32 6 atoms, 5 bonds, 1 residue, 1 model selected > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 3674 atoms, 3768 bonds, 484 residues, 1 model selected > select sel @ show sel target ab > style sel ball Changed 3674 atom styles > label sel attribute label_one_letter_code > label sel attribute label_specifier > close session > open ""/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/IFX Fab_TNFa > monomer.cxs"" opened ChimeraX session > open 3g4y fromDatabase pdb format mmcif Summary of feedback from opening 3g4y fetched from pdb --- notes | Fetching compressed mmCIF 3g4y from http://files.rcsb.org/download/3g4y.cif Fetching CCD 9CL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/9CL/9CL.cif Fetching CCD CMO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/CMO/CMO.cif Fetching CCD HEM from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/HEM/HEM.cif 3g4y title: Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloromethyl benzene bound to the XE4 cavity [more info...] Chain information for 3g4y #2 --- Chain | Description | UniProt A B | GLOBIN-1 | GLB1_SCAIN 1-146 Non-standard residues in 3g4y #2 --- 9CL — (chloromethyl)benzene CMO — carbon monoxide HEM — protoporphyrin IX containing Fe (HEME) > ui tool show Matchmaker > matchmaker #!2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_250117_ifx_fab_tnfa_monomer_model_0.cif, chain A (#1) with 3g4y, chain A (#2), sequence alignment score = 1.9 Fewer than 3 residues aligned; cannot match fold_250117_ifx_fab_tnfa_monomer_model_0.cif, chain A with 3g4y, chain A > ui tool show Matchmaker > matchmaker #!2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_250117_ifx_fab_tnfa_monomer_model_0.cif, chain A (#1) with 3g4y, chain A (#2), sequence alignment score = 1.9 Fewer than 3 residues aligned; cannot match fold_250117_ifx_fab_tnfa_monomer_model_0.cif, chain A with 3g4y, chain A > close session > open ""/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/IFX Fab_TNFa > monomer.cxs"" opened ChimeraX session > open 4g3y fromDatabase pdb format mmcif 4g3y title: Crystal structure of TNF-alpha in complex with Infliximab Fab fragment [more info...] Chain information for 4g3y #2 --- Chain | Description | UniProt C | Tumor necrosis factor | TNFA_HUMAN 1-157 H | infliximab Fab H | L | infliximab Fab L | 4g3y mmCIF Assemblies --- 1| author_defined_assembly 2| software_defined_assembly > ui tool show Matchmaker > matchmaker #2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_250117_ifx_fab_tnfa_monomer_model_0.cif, chain B (#1) with 4g3y, chain H (#2), sequence alignment score = 1113.8 RMSD between 216 pruned atom pairs is 0.564 angstroms; (across all 220 pairs: 0.775) > show sel target ab > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 9052 atoms, 9265 bonds, 1179 residues, 2 models selected > hide #* target a > show sel target ab > style sel stick Changed 9052 atom styles > style sel ball Changed 9052 atom styles > label sel attribute label_one_letter_code > label sel attribute label_specifier > hide sel target a > label sel attribute label_one_letter_code > label sel attribute label_specifier > label sel attribute label_one_letter_code > select #1/A:71 6 atoms, 5 bonds, 1 residue, 1 model selected > style sel stick Changed 6 atom styles > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 9052 atoms, 9265 bonds, 1179 residues, 2 models selected > style sel stick Changed 9052 atom styles > select #1/A:71 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/L:91 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:71 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #1/C:91 12 atoms, 10 bonds, 2 residues, 1 model selected > ui tool show Matchmaker > ui tool show Distances > style sel ball Changed 12 atom styles > select 9186 atoms, 9265 bonds, 1313 residues, 4 models selected > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 9052 atoms, 9265 bonds, 1179 residues, 2 models selected > style sel ball Changed 9052 atom styles > show sel target ab > select #1/A:73@CD2 1 atom, 1 residue, 1 model selected > select add #1/C:50@CB 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance #1/A:73@CD2 #1/C:50@CB Distance between fold_250117_ifx_fab_tnfa_monomer_model_0.cif #1/A HIS 73 CD2 and /C TYR 50 CB: 3.990Å Unsupported scale factor (0.000000) detected on Display0 > hide sel target a > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 9052 atoms, 9265 bonds, 1 pseudobond, 1179 residues, 3 models selected > hide (#!1-2 & sel) target a > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 9052 atoms, 9265 bonds, 1 pseudobond, 1179 residues, 3 models selected > show (#!1-2 & sel) target ab > select #1/A:104@CD 1 atom, 1 residue, 1 model selected > select add #1/C:49@CE 2 atoms, 2 residues, 1 model selected > distance #1/A:104@CD #1/C:49@CE Distance between fold_250117_ifx_fab_tnfa_monomer_model_0.cif #1/A GLU 104 CD and /C LYS 49 CE: 4.776Å > close session > open > /Users/erikookamoto/Downloads/fold_250121_certolizumab_fab_tnfa_monomer/fold_250121_certolizumab_fab_tnfa_monomer_model_0.cif Chain information for fold_250121_certolizumab_fab_tnfa_monomer_model_0.cif #1 --- Chain | Description A | . B | . C | . Computing secondary structure > select /A:1-214 1648 atoms, 1685 bonds, 214 residues, 1 model selected > select /B:1-229 1713 atoms, 1756 bonds, 229 residues, 1 model selected > select /C:1-157 1226 atoms, 1253 bonds, 157 residues, 1 model selected > color sel yellow > open 4g3y fromDatabase pdb format mmcif 4g3y title: Crystal structure of TNF-alpha in complex with Infliximab Fab fragment [more info...] Chain information for 4g3y #2 --- Chain | Description | UniProt C | Tumor necrosis factor | TNFA_HUMAN 1-157 H | infliximab Fab H | L | infliximab Fab L | 4g3y mmCIF Assemblies --- 1| author_defined_assembly 2| software_defined_assembly > close #2 > redo > open 5wux fromDatabase pdb format mmcif Summary of feedback from opening 5wux fetched from pdb --- note | Fetching compressed mmCIF 5wux from http://files.rcsb.org/download/5wux.cif 5wux title: TNFalpha-certolizumab Fab [more info...] Chain information for 5wux #2 --- Chain | Description | UniProt A C H | heavy | B D L | light | E F G | Tumor necrosis factor alpha | C1K3N5_HUMAN 1-157 5wux mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly > hide #1 models > show #1 models > select add #2 14019 atoms, 14360 bonds, 9 pseudobonds, 1825 residues, 3 models selected > select add #1 17380 atoms, 17801 bonds, 9 pseudobonds, 2268 residues, 3 models selected > select subtract #1 12793 atoms, 13107 bonds, 9 pseudobonds, 1668 residues, 2 models selected > cartoon hide (#!2 & sel) > surface hidePatches (#!2 & sel) > style sel sphere Changed 12793 atom styles > style sel sphere Changed 12793 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel ball Changed 12793 atom styles > select subtract #2 Nothing selected > hide atoms > show atoms > color bynucleotide > select add #2 12793 atoms, 13107 bonds, 9 pseudobonds, 1668 residues, 2 models selected > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel sphere Changed 12793 atom styles > style sel ball Changed 12793 atom styles > select add #1 17380 atoms, 17801 bonds, 9 pseudobonds, 2268 residues, 3 models selected > ui tool show Matchmaker > matchmaker #!2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_250121_certolizumab_fab_tnfa_monomer_model_0.cif, chain B (#1) with 5wux, chain H (#2), sequence alignment score = 1098 RMSD between 199 pruned atom pairs is 1.071 angstroms; (across all 212 pairs: 1.348) > select subtract #1 12793 atoms, 13107 bonds, 9 pseudobonds, 1668 residues, 2 models selected > close #2 > open /Users/erikookamoto/Downloads/5wux-sf.cif Summary of feedback from opening /Users/erikookamoto/Downloads/5wux-sf.cif --- warning | No mmCIF models found. > open /Users/erikookamoto/Downloads/5wux-sf.cif Summary of feedback from opening /Users/erikookamoto/Downloads/5wux-sf.cif --- warning | No mmCIF models found. > open 5wux fromDatabase pdb format mmcif 5wux title: TNFalpha-certolizumab Fab [more info...] Chain information for 5wux #2 --- Chain | Description | UniProt A C H | heavy | B D L | light | E F G | Tumor necrosis factor alpha | C1K3N5_HUMAN 1-157 5wux mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly > select add #2 12793 atoms, 13107 bonds, 9 pseudobonds, 1668 residues, 2 models selected > hide (#!2 & sel) target a > style (#!2 & sel) sphere Changed 12793 atom styles > hide #* target a > show (#!2 & sel) target ab > view > hide (#!2 & sel) target a > hide (#!2 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!2 & sel-residues) > show (#!2 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > undo > surface (#!2 & sel) > surface hidePatches (#!2 & sel) > select add #1 17380 atoms, 17801 bonds, 9 pseudobonds, 2268 residues, 12 models selected > select subtract #2 4587 atoms, 4694 bonds, 600 residues, 10 models selected > select add #2 17380 atoms, 17801 bonds, 9 pseudobonds, 2268 residues, 3 models selected > select subtract #1 12793 atoms, 13107 bonds, 9 pseudobonds, 1668 residues, 11 models selected > rainbow sel > color sel byhetero > color sel bychain > style sel sphere Changed 12793 atom styles > show sel surfaces > hide sel surfaces > show sel cartoons > color (#!2 & sel) light sea green > color (#!2 & sel) cyan > select subtract #2 9 models selected > ui tool show Matchmaker > matchmaker #!2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_250121_certolizumab_fab_tnfa_monomer_model_0.cif, chain B (#1) with 5wux, chain H (#2), sequence alignment score = 1098 RMSD between 199 pruned atom pairs is 1.071 angstroms; (across all 212 pairs: 1.348) > view > save /Users/erikookamoto/Desktop/image9.png supersample 3 > save ""/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/CZP_TNFa > monomer.cxs"" > open ""/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/RTX > Fab_CD20.cxs"" opened ChimeraX session > open 6vja fromDatabase pdb format mmcif Summary of feedback from opening 6vja fetched from pdb --- notes | Fetching compressed mmCIF 6vja from http://files.rcsb.org/download/6vja.cif Fetching CCD Y01 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/Y01/Y01.cif 6vja title: Structure of CD20 in complex with rituximab Fab [more info...] Chain information for 6vja #2 --- Chain | Description | UniProt C D | B-lymphocyte antigen CD20 | CD20_HUMAN 41-297 H I | Rituximab Fab heavy chain | L M | Rituximab Fab light chain | Non-standard residues in 6vja #2 --- Y01 — cholesterol hemisuccinate > hide sel surfaces > show sel cartoons > hide sel surfaces > select add #2 9726 atoms, 9988 bonds, 1257 residues, 2 models selected > select add #1 13016 atoms, 13361 bonds, 1694 residues, 2 models selected > select subtract #1 9342 atoms, 9593 bonds, 1210 residues, 1 model selected > hide sel surfaces > show sel cartoons > hide sel surfaces > hide sel target a > select add #1 13016 atoms, 13361 bonds, 1694 residues, 2 models selected > ui tool show Matchmaker > matchmaker #2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_250120_rtx_fab_cd20_extracellular_model_0.cif, chain A (#1) with 6vja, chain H (#2), sequence alignment score = 1142.9 RMSD between 103 pruned atom pairs is 0.571 angstroms; (across all 224 pairs: 9.363) > view > select subtract #2 3674 atoms, 3768 bonds, 484 residues, 1 model selected > select subtract #1 Nothing selected > select add #1 3674 atoms, 3768 bonds, 484 residues, 1 model selected > select add #2 13016 atoms, 13361 bonds, 1694 residues, 2 models selected > select subtract #1 9342 atoms, 9593 bonds, 1210 residues, 1 model selected > color sel cyan > select subtract #2 Nothing selected > save /Users/erikookamoto/Desktop/image10.png supersample 3 > open /Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/TCZ_IL-6.cxs opened ChimeraX session > open 8j6f fromDatabase pdb format mmcif Summary of feedback from opening 8j6f fetched from pdb --- notes | Fetching compressed mmCIF 8j6f from http://files.rcsb.org/download/8j6f.cif Fetching CCD NAG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif 8j6f title: Cryo-EM structure of the Tocilizumab Fab/IL-6R complex [more info...] Chain information for 8j6f #2 --- Chain | Description | UniProt B | IL6R-D2 peptide | IL6RA_HUMAN 103-112 H | Heavy chain of Tocilizumab Fab | I | Interleukin-6 receptor subunit alpha | IL6RA_HUMAN 1-365 L | Light chain of Tocilizumab Fab | Non-standard residues in 8j6f #2 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > select add #2 6551 atoms, 6729 bonds, 4 pseudobonds, 839 residues, 4 models selected > select add #1 9931 atoms, 10187 bonds, 4 pseudobonds, 1283 residues, 4 models selected > select subtract #1 3870 atoms, 3971 bonds, 4 pseudobonds, 497 residues, 3 models selected > select subtract #2 Nothing selected > select add #1 6061 atoms, 6216 bonds, 786 residues, 1 model selected > select add #2 9931 atoms, 10187 bonds, 4 pseudobonds, 1283 residues, 4 models selected > ui tool show Matchmaker > matchmaker #!2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_250120_tcz_fab_il6_model_0.cif, chain A (#1) with 8j6f, chain I (#2), sequence alignment score = 1325.1 RMSD between 64 pruned atom pairs is 0.771 angstroms; (across all 66 pairs: 0.850) > select subtract #1 3870 atoms, 3971 bonds, 4 pseudobonds, 497 residues, 3 models selected > select subtract #2 Nothing selected > view > view orient > view > ui tool show ""Side View"" > view orient > view > save /Users/erikookamoto/Desktop/image11.png supersample 3 > close session > open > /Users/erikookamoto/Downloads/fold_250121_certolizumab_fab_tnfa_trimer/fold_250121_certolizumab_fab_tnfa_trimer_model_0.cif Chain information for fold_250121_certolizumab_fab_tnfa_trimer_model_0.cif #1 --- Chain | Description A B C | . D E F | . G H I | . > hide surfaces > hide cartoons > show cartoons Computing secondary structure > select add #1 13761 atoms, 14082 bonds, 1800 residues, 1 model selected > hide sel surfaces > hide sel target a > show sel cartoons > hide sel cartoons > show sel cartoons Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 > select /G-I:157 27 atoms, 24 bonds, 3 residues, 1 model selected > select /G-I 3678 atoms, 3759 bonds, 471 residues, 1 model selected > color sel yellow > select /D-F:229 18 atoms, 15 bonds, 3 residues, 1 model selected > select /D-F 5139 atoms, 5268 bonds, 687 residues, 1 model selected > color sel dim gray > color sel light gray > select /A-C:180 21 atoms, 18 bonds, 3 residues, 1 model selected > select /A-C:142-180 906 atoms, 912 bonds, 117 residues, 1 model selected > select /A-C:214 21 atoms, 18 bonds, 3 residues, 1 model selected > select /A-C:71-214 3393 atoms, 3468 bonds, 432 residues, 1 model selected > select /A-C:1-214 4944 atoms, 5055 bonds, 642 residues, 1 model selected > color sel light gray > open 5wux fromDatabase pdb format mmcif 5wux title: TNFalpha-certolizumab Fab [more info...] Chain information for 5wux #2 --- Chain | Description | UniProt A C H | heavy | B D L | light | E F G | Tumor necrosis factor alpha | C1K3N5_HUMAN 1-157 5wux mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly > select add #2 17737 atoms, 18162 bonds, 9 pseudobonds, 2310 residues, 3 models selected > select add #1 26554 atoms, 27189 bonds, 9 pseudobonds, 3468 residues, 3 models selected > select subtract #1 12793 atoms, 13107 bonds, 9 pseudobonds, 1668 residues, 2 models selected > hide sel surfaces > hide (#!2 & sel) target a > show sel cartoons > color (#!2 & sel) cyan > select add #1 26554 atoms, 27189 bonds, 9 pseudobonds, 3468 residues, 3 models selected > ui tool show Matchmaker > matchmaker #!2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_250121_certolizumab_fab_tnfa_trimer_model_0.cif, chain A (#1) with 5wux, chain L (#2), sequence alignment score = 1080.8 RMSD between 213 pruned atom pairs is 0.686 angstroms; (across all 213 pairs: 0.686) > save ""/Users/erikookamoto/Library/CloudStorage/OneDrive-keio.jp/CZP_TNFa > trimer.cxs"" > select subtract #1 12793 atoms, 13107 bonds, 9 pseudobonds, 1668 residues, 2 models selected > select subtract #2 Nothing selected > view > save /Users/erikookamoto/Desktop/image12.png supersample 3 > close session > open ""/Users/erikookamoto/Library/CloudStorage/OneDrive- > keio.jp/Trastuzumab_HER2 extracellular.cxs"" opened ChimeraX session > open 6oge fromDatabase pdb format mmcif Summary of feedback from opening 6oge fetched from pdb --- notes | Fetching compressed mmCIF 6oge from http://files.rcsb.org/download/6oge.cif Fetching CCD BMA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif Fetching CCD MAN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif 6oge title: Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex [more info...] Chain information for 6oge #2 --- Chain | Description | UniProt A | Receptor tyrosine-protein kinase erbB-2 | ERBB2_HUMAN 23-644 B | Pertuzumab FAB LIGHT CHAIN | IGKC_HUMAN 108-214 C | Pertuzumab FAB HEAVY CHAIN | IGG1_HUMAN 103-216 D | Trastuzumab FAB LIGHT CHAIN | IGKC_HUMAN 108-214 E | Trastuzumab FAB HEAVY CHAIN | Q6GMX6_HUMAN 109-220 Non-standard residues in 6oge #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > hide sel surfaces > select add #2 16333 atoms, 16765 bonds, 1 pseudobond, 2128 residues, 3 models selected > select add #1 19633 atoms, 20144 bonds, 1 pseudobond, 2562 residues, 3 models selected > select subtract #1 11494 atoms, 11809 bonds, 1 pseudobond, 1498 residues, 2 models selected > style sel sphere Changed 11494 atom styles > style sel sphere Changed 11494 atom styles > hide sel surfaces > show sel cartoons > hide sel surfaces > hide (#!2 & sel) target a > ui tool show Matchmaker > matchmaker #!2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_trastuzumab_her2_extracellular_model_0.cif, chain A (#1) with 6oge, chain A (#2), sequence alignment score = 3032.8 RMSD between 461 pruned atom pairs is 0.964 angstroms; (across all 619 pairs: 3.312) > select subtract #2 Nothing selected > select add #2 11494 atoms, 11809 bonds, 1 pseudobond, 1498 residues, 2 models selected > color (#!2 & sel) cyan > select subtract #2 Nothing selected > save /Users/erikookamoto/Desktop/image13.png supersample 3 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,12 Model Number: MRXT3J/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.81.1 OS Loader Version: 10151.81.1 Software: System Software Overview: System Version: macOS 14.3 (23D2057) Kernel Version: Darwin 23.3.0 Time since boot: 36日 28分 Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX