id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17472 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-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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""SIRI_MEMORY_SYNC_CONFIG"" : ""6526e111d0c9ce2f459b54a8"" }, ""deploymentId"" : 240000015 } ], ""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/aleon/Desktop/ModelBuilding/3G11new/RealSpaceRefine_17/3G11_RS16-coot-0-combined_real_space_refined_017.pdb Chain information for 3G11_RS16-coot-0-combined_real_space_refined_017.pdb #1 --- Chain | Description A | No description available B D F | No description available C | No description available E | No description available H | No description available L | No description available > ui tool show ""Show Sequence Viewer"" > sequence chain /L Alignment identifier is 1/L > select /L:34 10 atoms, 9 bonds, 1 residue, 1 model selected > select /L:34 10 atoms, 9 bonds, 1 residue, 1 model selected > close > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/3G11-reviewable/3G11_RS22_kabat.pdb"" Chain information for 3G11_RS22_kabat.pdb #1 --- Chain | Description A | No description available B D F | No description available C | No description available E | No description available H | No description available L | No description available > close > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/6G8-reviewable/6G8_RSR_kabat_20.pdb"" Chain information for 6G8_RSR_kabat_20.pdb #1 --- Chain | Description A C | No description available B D F | No description available E | No description available H | No description available L | No description available > close > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/6H4-reviewable/6H4_RS56_kabat.pdb"" Chain information for 6H4_RS56_kabat.pdb #1 --- Chain | Description A | No description available B D F | No description available C E | No description available H | No description available L | No description available > close > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/5G01-reviewable/5G01_RS35_kabat.pdb"" Chain information for 5G01_RS35_kabat.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available H | No description available L | No description available > close > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/6H4-reviewable/6H4_RS56_kabat.pdb"" Chain information for 6H4_RS56_kabat.pdb #1 --- Chain | Description A | No description available B D F | No description available C E | No description available H | No description available L | No description available > close > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/6G8-reviewable/6G8_RSR_kabat_20.pdb"" Chain information for 6G8_RSR_kabat_20.pdb #1 --- Chain | Description A C | No description available B D F | No description available E | No description available H | No description available L | No description available > close > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/3G11-reviewable/3G11_RS22_kabat.pdb"" Chain information for 3G11_RS22_kabat.pdb #1 --- Chain | Description A | No description available B D F | No description available C | No description available E | No description available H | No description available L | No description available > close > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/6H4-reviewable/6H4_RS56_kabat.pdb"" Chain information for 6H4_RS56_kabat.pdb #1 --- Chain | Description A | No description available B D F | No description available C E | No description available H | No description available L | No description available > ui tool show ""Change Chain IDs"" > cloe Unknown command: cloe > close > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/6H4-reviewable/6H4_RS56_kabat.pdb"" Chain information for 6H4_RS56_kabat.pdb #1 --- Chain | Description A | No description available B D F | No description available C E | No description available H | No description available L | No description available > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/3G11-reviewable/3G11_RS22_kabat.pdb"" Chain information for 3G11_RS22_kabat.pdb #2 --- Chain | Description A | No description available B D F | No description available C | No description available E | No description available H | No description available L | No description available > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/5G01-reviewable/5G01_RS35_kabat.pdb"" Chain information for 5G01_RS35_kabat.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available H | No description available L | No description available > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/DishaH15CryoModels/ManuscriptFiles/EMDBDepos/6G8-reviewable/6G8_RSR_kabat_20.pdb"" Chain information for 6G8_RSR_kabat_20.pdb #4 --- Chain | Description A C | No description available B D F | No description available E | No description available H | No description available L | No description available > hide #!4 models > hide #!3 models > show #!3 models > show #!4 models > hide atoms > show cartoons > lighting soft > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 104644 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > mmaker #2/A to #1/A 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 6H4_RS56_kabat.pdb, chain A (#1) with 3G11_RS22_kabat.pdb, chain A (#2), sequence alignment score = 1462.7 RMSD between 318 pruned atom pairs is 0.740 angstroms; (across all 321 pairs: 0.766) > mmaker #3/A to #1/A 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 6H4_RS56_kabat.pdb, chain A (#1) with 5G01_RS35_kabat.pdb, chain A (#3), sequence alignment score = 1481 RMSD between 310 pruned atom pairs is 0.875 angstroms; (across all 321 pairs: 0.962) > mmaker #4/A to #1/A 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 6H4_RS56_kabat.pdb, chain A (#1) with 6G8_RSR_kabat_20.pdb, chain A (#4), sequence alignment score = 1471.9 RMSD between 323 pruned atom pairs is 0.679 angstroms; (across all 325 pairs: 0.701) > select clear Drag select of 2558 residues > select up 51769 atoms, 52197 bonds, 3356 residues, 4 models selected > select up 92023 atoms, 92988 bonds, 5935 residues, 4 models selected > color sel light grey > select clear Drag select of 1122 residues, 3 pseudobonds > select up 30560 atoms, 30808 bonds, 3 pseudobonds, 2021 residues, 7 models selected > select up 61307 atoms, 61949 bonds, 3 pseudobonds, 3955 residues, 7 models selected > color sel grey > select clear > save > /Users/aleon/Desktop/ModelBuilding/FigureImages/FinalModelFigures/AllH15ModelsAligned.cxs > includeMaps true > open > /Users/aleon/Desktop/ModelBuilding/6F6new/6F6_with6G8H15_chainRefined_newStart.pdb Chain information for 6F6_with6G8H15_chainRefined_newStart.pdb #5 --- Chain | Description A C E | No description available B D F | No description available H | No description available L | No description available > hide atoms > show cartoons > mmaker #5/E to #1/A 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 6H4_RS56_kabat.pdb, chain A (#1) with 6F6_with6G8H15_chainRefined_newStart.pdb, chain E (#5), sequence alignment score = 1412.5 RMSD between 324 pruned atom pairs is 0.697 angstroms; (across all 325 pairs: 0.706) > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 13443 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models Drag select of 1014 residues > select up 8766 atoms, 8901 bonds, 1118 residues, 1 model selected > select up 11661 atoms, 11882 bonds, 1488 residues, 1 model selected > color sel grey > select clear > select #5/F:445 5 atoms, 4 bonds, 1 residue, 1 model selected > select #5/E:82 7 atoms, 7 bonds, 1 residue, 1 model selected > select add #5/F:438 14 atoms, 13 bonds, 2 residues, 1 model selected > select up 493 atoms, 499 bonds, 59 residues, 1 model selected > select up 3887 atoms, 3959 bonds, 496 residues, 1 model selected > color sel light grey > select clear > show #!1 models > hide #!1 models > show #!2 models > show #!4 models > hide #5 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > save > /Users/aleon/Desktop/ModelBuilding/FigureImages/FinalModelFigures/AllH15ModelsAligned.cxs > includeMaps true > hide #!2 models > show #!2 models > hide #!4 models Drag select of 745 residues, 2 pseudobonds > select up 14131 atoms, 14237 bonds, 2 pseudobonds, 908 residues, 2 models selected > select up 22691 atoms, 22928 bonds, 2 pseudobonds, 1463 residues, 2 models selected > hide sel > hide sel cartoons > show #!4 models > select clear Drag select of 616 residues, 2 pseudobonds > select up 13410 atoms, 13519 bonds, 2 pseudobonds, 859 residues, 2 models selected > select up 23259 atoms, 23505 bonds, 2 pseudobonds, 1499 residues, 2 models selected > show sel surfaces > hide sel cartoons > select clear > color #BB3C19 #2/H Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select #2/H 1776 atoms, 1801 bonds, 119 residues, 1 model selected > color sel #BB3C19 > select #2/L 1680 atoms, 1705 bonds, 111 residues, 1 model selected > color sel #FF7F50 > select #3/H 1856 atoms, 1876 bonds, 123 residues, 1 model selected > select #4/H 1782 atoms, 1806 bonds, 119 residues, 1 model selected > color sel #C13C5F > select #4/L 1678 atoms, 1700 bonds, 111 residues, 1 model selected > color sel #D16783 > select clear > set bgColor white > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!1 models > hide #!1 models > show #!3 models > show #!1 models > hide #!2 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!3 models > select #1/H 1694 atoms, 1717 bonds, 115 residues, 1 model selected > color sel #558E72 > color sel #98C6B0 > select #1/H 1694 atoms, 1717 bonds, 115 residues, 1 model selected > color sel #558E72 > select #1/L 1732 atoms, 1756 bonds, 113 residues, 1 model selected > color sel #98C6B0 > select clear > hide #!1 models > hide #!4 models > show #!4 models > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > select #3/H 1856 atoms, 1876 bonds, 123 residues, 1 model selected > color sel #DAD432 > select #3/L 1636 atoms, 1658 bonds, 108 residues, 1 model selected > color sel #FFFB81 > show #!2 models > hide #!2 models > show #!2 models > hide #!4 models > show #!4 models > hide #!3 models > select #2/H 1776 atoms, 1801 bonds, 119 residues, 1 model selected > color sel #2D609F > select #2/L 1680 atoms, 1705 bonds, 111 residues, 1 model selected > color sel #74A8E7 > select clear > save > /Users/aleon/Desktop/ModelBuilding/FigureImages/FinalModelFigures/3G11_6G8_Overlay.cxs > includeMaps true > ui tool show ""Side View"" Drag select of 167 residues > select up 4737 atoms, 4791 bonds, 309 residues, 2 models selected > select up 6916 atoms, 7012 bonds, 460 residues, 2 models selected > hide sel cartoons > select #2/H:29-35,51-47,100A-95 124 atoms, 128 bonds, 7 residues, 1 model selected > show sel cartoons > select #2/H:29-35,47-51,95-100A 304 atoms, 311 bonds, 19 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #2/H:29-35,51-57,95-100A 333 atoms, 340 bonds, 22 residues, 1 model selected > show sel cartoons > select #2/H:25-35,51-57,95-100A 383 atoms, 391 bonds, 26 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #2/H:28-35,51-57,95-100A 344 atoms, 351 bonds, 23 residues, 1 model selected > show sel cartoons > select clear > select #4/H:28-35,51-57,95-100A 352 atoms, 359 bonds, 23 residues, 1 model selected > show sel cartoons > select clear > select #4/L:27C-31,90-95 179 atoms, 181 bonds, 12 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #4/L:27C-31,91-95 162 atoms, 164 bonds, 11 residues, 1 model selected > show sel cartoons > select #2/L:27C-31,91-95 161 atoms, 163 bonds, 11 residues, 1 model selected > show sel cartoons > select clear > lighting soft > graphics silhouettes true > lighting gentle > lighting soft > select #4/E:207@CA 1 atom, 1 residue, 1 model selected > select add #4/C:207@N 2 atoms, 2 residues, 2 models selected > select up 14 atoms, 12 bonds, 2 residues, 3 models selected > select up 166 atoms, 164 bonds, 12 residues, 3 models selected > select up 10041 atoms, 10150 bonds, 657 residues, 3 models selected > hide sel surfaces > select #4/F:423@CD 1 atom, 1 residue, 1 model selected > select add #4/D:414@C 2 atoms, 2 residues, 2 models selected > select down 2 atoms, 2 residues, 3 models selected > select up 34 atoms, 32 bonds, 2 residues, 3 models selected > select up 634 atoms, 636 bonds, 38 residues, 3 models selected > hide sel surfaces > select #4/F:429@CG2 1 atom, 1 residue, 1 model selected > select up 16 atoms, 15 bonds, 1 residue, 2 models selected > select up 837 atoms, 843 bonds, 51 residues, 2 models selected > select up 2747 atoms, 2774 bonds, 172 residues, 2 models selected > hide sel surfaces > select #4/D:404@O 1 atom, 1 residue, 1 model selected > select up 19 atoms, 18 bonds, 1 residue, 2 models selected > select up 291 atoms, 291 bonds, 18 residues, 2 models selected > select up 2747 atoms, 2774 bonds, 172 residues, 2 models selected > hide sel surfaces > graphics silhouettes false > graphics silhouettes true > show #!3 models > hide #!3 models > save 6G8_classCDRs.png supersample 8 transparentBackground true > select #2/H:35 17 atoms, 17 bonds, 1 residue, 1 model selected > select add #4/H:35 34 atoms, 34 bonds, 2 residues, 2 models selected > hide sel cartoons > select #2/H:28 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #4/H:28 22 atoms, 20 bonds, 2 residues, 2 models selected > hide sel cartoons > select #2/H:29 20 atoms, 20 bonds, 1 residue, 1 model selected > select add #4/H:29 40 atoms, 40 bonds, 2 residues, 2 models selected > hide sel cartoons > save 6G8_classCDRs.png supersample 8 transparentBackground true > hide #!2 models > select #4/A 5002 atoms, 5056 bonds, 1 pseudobond, 327 residues, 2 models selected > hide sel surfaces > select #4/B:423@OE2 1 atom, 1 residue, 1 model selected > select up 15 atoms, 14 bonds, 1 residue, 2 models selected > select up 298 atoms, 299 bonds, 18 residues, 2 models selected > select up 2722 atoms, 2748 bonds, 171 residues, 2 models selected > hide sel surfaces > select #4/A 5002 atoms, 5056 bonds, 1 pseudobond, 327 residues, 2 models selected > show sel cartoons > select clear > select #4/A:166,167,168,169,206 75 atoms, 73 bonds, 5 residues, 1 model selected > show sel atoms > color sel byhetero > select #4/H:33,56,52,99,100,97 106 atoms, 106 bonds, 6 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > save > /Users/aleon/Desktop/ModelBuilding/FigureImages/FinalModelFigures/6G8_Class_HC_interactions.cxs > includeMaps true > select #4/H:33,56,52,99,100,97 106 atoms, 106 bonds, 6 residues, 1 model selected > ui tool show H-Bonds > select #4/H:33,56,52,99,100,97 106 atoms, 106 bonds, 6 residues, 1 model selected > select #4/A:166,167,168,169,206 75 atoms, 73 bonds, 5 residues, 1 model selected > select #4/H:33,56,52,99,100,97 106 atoms, 106 bonds, 6 residues, 1 model selected > /A:166,167,168,169,206 Unknown command: /A:166,167,168,169,206 > select #4/H:33,56,52,99,100,97,#4/A:166,167,168,169,206 Expected an objects specifier or a keyword > select #4/H:33,56,52,99,100,97 106 atoms, 106 bonds, 6 residues, 1 model selected > select H 51933 atoms, 6855 residues, 4 models selected > hide sel & #!4 atoms > select #4/H:33,56,52,99,100,97 106 atoms, 106 bonds, 6 residues, 1 model selected > hbonds sel color #000000 interModel false intraMol false intraRes false > reveal true 3 hydrogen bonds found > ui tool show H-Bonds > hbonds delete > select H 51933 atoms, 6855 residues, 4 models selected > hide sel & #!4 atoms > select clear > select #4/L 1678 atoms, 1700 bonds, 111 residues, 1 model selected > hide sel atoms > hide sel cartoons > select clear > select #4/A:206 14 atoms, 13 bonds, 1 residue, 1 model selected > select add #4/H:97@CD1 15 atoms, 13 bonds, 2 residues, 2 models selected > select #4/H:97@CD1 1 atom, 1 residue, 1 model selected > select clear > select add #4/A:206 14 atoms, 13 bonds, 1 residue, 1 model selected > select add #4/H:97 35 atoms, 34 bonds, 2 residues, 2 models selected > hbonds sel color #424242 restrict both interModel false intraMol false > intraRes false reveal true 0 hydrogen bonds found > show sel atoms > hbonds sel color #424242 restrict both interModel false intraMol false > intraRes false reveal true 0 hydrogen bonds found > hbonds sel color #424242 restrict both interModel false distSlop 0.5 > intraMol false intraRes false reveal true 0 hydrogen bonds found > hbonds sel color #424242 restrict both interModel false distSlop 0.6 > intraMol false intraRes false reveal true 0 hydrogen bonds found > hbonds sel color #424242 restrict both interModel false distSlop 0.8 > intraMol false intraRes false reveal true 0 hydrogen bonds found > hbonds sel color #424242 restrict both interModel false angleSlop 30.0 > intraMol false intraRes false reveal true 0 hydrogen bonds found > hbonds sel color #424242 interModel false angleSlop 30.0 intraMol false > intraRes false reveal true 0 hydrogen bonds found > hbonds sel color #424242 interModel false angleSlop 50.0 intraMol false > intraRes false reveal true 1 hydrogen bonds found > select clear > select #4/H:97 21 atoms, 21 bonds, 1 residue, 1 model selected > hbonds sel color #797979 interModel false angleSlop 50.0 intraMol false > intraRes false reveal true 1 hydrogen bonds found > hbonds sel color #919191 interModel false angleSlop 50.0 intraMol false > intraRes false reveal true 1 hydrogen bonds found > select clear > select #4/H:33,56,52,99,100,97 again Expected a keyword > select #4/H:33,56,52,99,100,97 106 atoms, 106 bonds, 6 residues, 1 model selected > hbonds sel color #919191 interModel false angleSlop 50.0 intraMol false > intraRes false reveal true 5 hydrogen bonds found > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > hbonds sel color #797979 interModel false angleSlop 50.0 intraMol false > intraRes false reveal true 1 hydrogen bonds found > hide sel atoms > select #4/H:33,56,52,99,100,97 106 atoms, 106 bonds, 6 residues, 1 model selected > hbonds sel color #797979 interModel false angleSlop 50.0 intraMol false > intraRes false reveal true 5 hydrogen bonds found > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > select H 51933 atoms, 6855 residues, 4 models selected > hide sel & #!4 atoms ===== 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 - 88.1 OpenGL renderer: Apple M1 Max 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 Pro Model Identifier: MacBookPro18,2 Model Number: Z14W00106LL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 22 days, 19 hours, 42 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 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