id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20111 Crash on Mac waking from sleep kelvin.lau@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.3.1-arm64-arm-64bit ChimeraX Version: 1.10 (2025-06-26 08:57:52 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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""com.apple.Foundation"", ""size"" : 16399392, ""uuid"" : ""187e7913-b154-30a7-8070-852767aac3cf"", ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""4302"" } ], ""sharedCache"" : { ""base"" : 6719340544, ""size"" : 5820792832, ""uuid"" : ""f3e3cb1b-1c09-3cc5-ad72-f0800f1f475f"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=2.1G resident=0K(0%) swapped_out_or_unallocated=2.1G(100%)\nWritable regions: Total=3.5G written=21.2M(1%) resident=2747K(0%) swapped_out=18.6M(1%) unallocated=3.5G(99%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \n.note.gnu.proper 320 1 \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nAttributeGraph Data 1024K 1 \nCG image 720K 21 \nColorSync 144K 9 \nCoreAnimation 4592K 212 \nCoreGraphics 80K 5 \nCoreServices 624K 2 \nCoreUI image data 5392K 40 \nFoundation 48K 2 \nKernel Alloc Once 48K 2 \nMALLOC 2.8G 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""roots_installed"" : 0, ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""644114de41e7236e6177f9bd"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000013 }, { ""rolloutId"" : ""67fd77fe1f9da9148f70d6ed"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000020 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== > graphics silhouettes true > lighting soft > windowsize 800 800 > ui tool hide ""command line interface"" > ui tool show clix UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/kelvinlau/Desktop/RhGB07-full/v7/RBD zoomed in-more- > clade1-v7.cxs"" format session Opened 103_zflipped.ccp4 as #2, grid size 300,300,300, pixel 1.38, shown at level 0.184, step 1, values float32 Opened 103_sharp_zflipped.ccp4 as #3, grid size 300,300,300, pixel 1.38, shown at level 0.239, step 1, values float32 Opened 103_zflipped.ccp4 1 as #6.2, grid size 300,300,300, pixel 1.38, shown at level 0.19, step 1, values float32 > view name session-start opened ChimeraX session > ui tool show ""Command Line Interface"" > toolshed show > ui tool show ""Command Line Interface"" > ui tool show clix > rename #11 sarscov2closed > rename #12 5x58 > rename #12 sarscov1 closed Expected a keyword > rename #12 sarscov1closed > hide #!11 models > hide #!12 models > show #!10 models > show #!9 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!9 models > show #!9 models > hide #!9 models > hide #!10 models > hide #!4 models > show #!12 models > hide #!11 models > show #!11 models > hide #!11 models > open /Users/kelvinlau/Downloads/7DF3.pdb 7DF3.pdb title: Sars-cov-2 S trimer, S-closed [more info...] Chain information for 7DF3.pdb #13 --- Chain | Description | UniProt A B C | spike glycoprotein | SPIKE_SARS2 1-1208 Non-standard residues in 7DF3.pdb #13 --- NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) > show #!4 models > hide #!4 models > show #!4 models > mmaker #13 to #4 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 30B-RBD-only.pdb, chain A (#4) with 7DF3.pdb, chain A (#13), sequence alignment score = 636.7 RMSD between 163 pruned atom pairs is 1.064 angstroms; (across all 179 pairs: 1.808) > close #11 > rename #13 sarscov2closed > color #12 #5272aaff > color #13 #b44e66ff > hide #!4 models > hide #!13 models > show #!9 models > hide #!12 models > hide #!9 models > show #!12 models > select #12/A:320-503 1480 atoms, 1528 bonds, 184 residues, 1 model selected > show #!9 models > select ~sel & ##selected 23785 atoms, 24387 bonds, 9 pseudobonds, 3017 residues, 2 models selected > hide sel atoms > hide sel cartoons > hide #!9 models > close #9 > hide sel cartoons > show sel atoms > hide sel atoms > select clear Drag select of 56 atoms, 184 residues, 50 bonds > hide sel cartoons > hide sel atoms > show sel atoms > style sel ball Changed 1480 atom styles > style sel sphere Changed 1480 atom styles > style sel ball Changed 1480 atom styles > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > select clear > hide #!12 models > show #!10 models > show #!13 models > select #13/A:333-516 1469 atoms, 1513 bonds, 184 residues, 1 model selected > hide #!10 models > select ~sel & ##selected 25126 atoms, 25787 bonds, 12 pseudobonds, 3158 residues, 2 models selected > hide sel cartoons > hide sel atoms > select clear Drag select of 32 atoms, 184 residues, 26 bonds > hide sel atoms > hide sel cartoons > show sel atoms > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > style sel ball Changed 1469 atom styles > select clear > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > close #10 > show #!12 models > show #!4 models > save ""/Users/kelvinlau/Desktop/RhGB07-full/v7/RBD zoomed in-more- > clade1-v7.cxs"" > save /Users/kelvinlau/Desktop/image1.png supersample 3 > ui tool show ""Side View"" > save /Users/kelvinlau/Desktop/image2.png supersample 3 > save /Users/kelvinlau/Desktop/image3.png supersample 3 > hide #!12 models > hide #!13 models > hide #!4 models > show #!1 models > hide #!1 atoms > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > show #!2 models > hide #!3 models > ui tool show ""Show Sequence Viewer"" FYI: command is replacing existing command: ""sequence align"" FYI: command is replacing existing command: ""sequence associate"" FYI: command is replacing existing command: ""sequence chain"" FYI: command is replacing existing command: ""sequence disassociate"" FYI: command is replacing existing command: ""sequence dissociate"" FYI: command is replacing existing command: ""sequence expandsel"" FYI: command is replacing existing command: ""sequence header"" FYI: command is replacing existing command: ""sequence identity"" FYI: command is replacing existing command: ""sequence match"" FYI: command is replacing existing command: ""sequence refseq"" FYI: command is replacing existing command: ""sequence refreshAttrs"" FYI: command is replacing existing command: ""sequence rename"" FYI: command is replacing existing command: ""sequence update"" FYI: command is replacing existing command: ""sequence grid"" FYI: command is replacing existing command: ""sequence viewer"" > sequence chain #1/A #1/B #1/C Alignment identifier is 1 > select #1/A-C:201 30 atoms, 30 bonds, 3 residues, 1 model selected > select #1/A-C:201-204 117 atoms, 120 bonds, 12 residues, 1 model selected > volume #2 color #b2b2b280 > select > #1/A-C:32-34,51-59,65-70,92-98,103-109,118-123,127-133,135-137,144-146,149-152,156-159,184-193,196-204,220-226,233-238,255-260,262-270,276-281,302-305,345-349,368-372,387-394,423-429,440-442,479-481,496-502,526-530,535-539,563-566,571-574,583-587,598-601,632-634,638-641,654-657,660-664,675-679,695-697,700-711,716-718,842-844,1030-1039,1042-1053,1056-1058,1071-1073,1077-1080,1085-1088,1103-1105 6435 atoms, 6504 bonds, 786 residues, 1 model selected > select #1/A-C:106 42 atoms, 45 bonds, 3 residues, 1 model selected > select #1/A-C:106 42 atoms, 45 bonds, 3 residues, 1 model selected > select #1/A-C:102 21 atoms, 18 bonds, 3 residues, 1 model selected > select #1/A-C:102 21 atoms, 18 bonds, 3 residues, 1 model selected > select #1/A-C:102 21 atoms, 18 bonds, 3 residues, 1 model selected > select #1/A-C:102,106 63 atoms, 63 bonds, 6 residues, 1 model selected > select #1/A-C:102,106,121 87 atoms, 84 bonds, 9 residues, 1 model selected > select #1/A-C:102,106,121,123 111 atoms, 105 bonds, 12 residues, 1 model selected > select #1/A-C:102,106,121,123,128 135 atoms, 126 bonds, 15 residues, 1 model selected > select #1/A-C:102,106,121,123,128,186 168 atoms, 156 bonds, 18 residues, 1 model selected > select #1/A-C:102,106,121,123,128,186,188 198 atoms, 186 bonds, 21 residues, 1 model selected > select #1/A-C:102,106,121,123,128,186,188,203 234 atoms, 222 bonds, 24 residues, 1 model selected > select #1/A-C:102,106,121,123,128,186,188,203,222-223 291 atoms, 279 bonds, 30 residues, 1 model selected > show sel atoms > style sel stick Changed 291 atom styles > color sel byhetero > name sel bili ""sel"" is reserved and cannot be redefined > select name bili Expected an objects specifier or a keyword > name bili sel > select #1/A-C:102,106,121,123,128,186,188,203,222-223 291 atoms, 279 bonds, 30 residues, 1 model selected > select #1/A-C:102,106,121,123,128,186,188,203,222-223 291 atoms, 279 bonds, 30 residues, 1 model selected > select #1/A-C:102-104,106,121,123,128,186,188,203,222-223 345 atoms, 333 bonds, 36 residues, 1 model selected > select #1/A-C:102-104,106,121,123,128,186,188,203,222-223 345 atoms, 333 bonds, 36 residues, 1 model selected > select #1/A-C:102-104,106,121,123,128,186,188,203,222-223 345 atoms, 333 bonds, 36 residues, 1 model selected > select #1/A-C:102-104,106,121,123,128,186,188,203,222-223 345 atoms, 333 bonds, 36 residues, 1 model selected > hide sel atoms > select #1/A-C:103,106,121,123,128,186,188,203,222-223 291 atoms, 279 bonds, 30 residues, 1 model selected > show sel atoms > style sel stick Changed 291 atom styles > select clear > select #1/A-C:90 30 atoms, 30 bonds, 3 residues, 1 model selected > select #1/A-C:90-282 4248 atoms, 4368 bonds, 3 pseudobonds, 537 residues, 2 models selected > ui tool show ""Surface Zone"" > surface zone #2 nearAtoms #1 distance 5 > surface zone #2 nearAtoms sel distance 5 > select clear > recenter Unknown command: recenter > center Unknown command: center > show #!3 models > hide #!3 models > select #1/B:33 11 atoms, 11 bonds, 1 residue, 1 model selected > cofr sel > select clear > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > select #1/A:103 7 atoms, 6 bonds, 1 residue, 1 model selected > cofr sel > select clear > volume #2 level 0.1591 > volume #2 level 0.1528 > volume #2 level 0.1864 > select #1/A-C:103,106,121,123,128,186,188,203,222-223 291 atoms, 279 bonds, 30 residues, 1 model selected > ui tool show ""Color Actions"" > color sel #b44e66ff target a > color sel byhetero target a > select clear > save /Users/kelvinlau/Desktop/image1.png supersample 3 No atoms selected for zoning > save /Users/kelvinlau/Desktop/image2.png supersample 3 > hide #!2 models > save /Users/kelvinlau/Desktop/RhGB07-full/v7/biliverdin.cxs > select #1/A-C:383 18 atoms, 15 bonds, 3 residues, 1 model selected > select #1/A-C:383 18 atoms, 15 bonds, 3 residues, 1 model selected > select #1/A-C:383 18 atoms, 15 bonds, 3 residues, 1 model selected > select #1/A-C:383,424-425 57 atoms, 51 bonds, 9 residues, 1 model selected Drag select of 2 residues > select #1/A-C:383 18 atoms, 15 bonds, 3 residues, 1 model selected > select #1/A-C:383 18 atoms, 15 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 18 atom styles > hide sel atoms > select #1/A-C:371 18 atoms, 15 bonds, 3 residues, 1 model selected > select #1/A-C:371 18 atoms, 15 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 18 atom styles > hide sel atoms > select #1/A-C:327,371 36 atoms, 30 bonds, 6 residues, 1 model selected > select #1/A-C:327 18 atoms, 15 bonds, 3 residues, 1 model selected > select #1/A-C:325-327 69 atoms, 66 bonds, 9 residues, 1 model selected > select #1/A-C:327 18 atoms, 15 bonds, 3 residues, 1 model selected > select #1/A-C:327 18 atoms, 15 bonds, 3 residues, 1 model selected > select #1/A-C:327,352 36 atoms, 33 bonds, 6 residues, 1 model selected > show sel atoms > style sel stick Changed 36 atom styles > surface unzone #2 > show #!2 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/B #1/C Alignment identifier is 2 > sequence chain #13/A #13/B #13/C Alignment identifier is 3 > ui tool show ""Show Sequence Viewer"" > sequence chain #13/A #13/B #13/C Alignment identifier is 2 > hide #!1 models > hide #!2 models > show #!6 models > show #!4 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > select add #1 27102 atoms, 27867 bonds, 6 pseudobonds, 3399 residues, 2 models selected > select subtract #1 Nothing selected > hide #!4 models > show #!4 models > show #!6 models > hide #!6.2 models > show #!6.2 models > hide #!6 models Drag select of 181 atoms, 180 pseudobonds > show #!6 models > ui tool show ""Color Zone"" > color zone #6.2 near #4 distance 8.3 > volume splitbyzone #6.2 Opened 103_zflipped.ccp4 1 0 as #9.1, grid size 300,300,300, pixel 1.38, shown at level 0.19, step 1, values float32 Opened 103_zflipped.ccp4 1 1 as #9.2, grid size 300,300,300, pixel 1.38, shown at level 0.19, step 1, values float32 > hide #!9.1 models > show #!9.1 models > close #9.1 > hide #!6 models > show #!6 models > close #6 > hide #!9.2 models > show #!9.2 models > color #9.2 #55627080 models > select clear Drag select of 9.2 103_zflipped.ccp4 1 1 , 34 atoms, 36 pseudobonds > cofr sel > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #4/A Alignment identifier is 4/A > select #4/A:366 11 atoms, 11 bonds, 1 residue, 1 model selected > select #4/A:366 11 atoms, 11 bonds, 1 residue, 1 model selected > select #4/A:366,369 22 atoms, 22 bonds, 2 residues, 1 model selected > select #4/A:338,366,369 33 atoms, 33 bonds, 3 residues, 1 model selected > select #4/A:338,366,369 33 atoms, 33 bonds, 3 residues, 1 model selected > select clear > show #!4 cartoons > select #4/A:338 11 atoms, 11 bonds, 1 residue, 1 model selected > select #4/A:338 11 atoms, 11 bonds, 1 residue, 1 model selected > select #4/A:338,366 22 atoms, 22 bonds, 2 residues, 1 model selected > select #4/A:352 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/A:352 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/A:327,352 12 atoms, 11 bonds, 2 residues, 1 model selected Drag select of 9.2 103_zflipped.ccp4 1 1 , 1 residues > select #4/A:327-328 13 atoms, 13 bonds, 2 residues, 1 model selected > select #4/A:327-328 13 atoms, 13 bonds, 2 residues, 1 model selected > select #4/A:328 7 atoms, 7 bonds, 1 residue, 1 model selected > select #4/A:327-328 13 atoms, 13 bonds, 2 residues, 1 model selected > select #4/A:327 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/A:327 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/A:327,352 12 atoms, 11 bonds, 2 residues, 1 model selected > toolshed show > ui tool show ""Show Sequence Viewer"" > sequence chain #4/A Alignment identifier is 4/A > open > /Users/kelvinlau/Downloads/clustalo-I20260401-175019-0503-45788964-p1m.aln- > clustal_num Unrecognized file suffix '.aln-clustal_num' > open > /Users/kelvinlau/Downloads/clustalo-I20260401-175019-0503-45788964-p1m.aln Summary of feedback from opening /Users/kelvinlau/Downloads/clustalo-I20260401-175019-0503-45788964-p1m.aln --- notes | Alignment identifier is clustalo-I20260401-175019-0503-45788964-p1m.aln Associated trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb chain A to rhgb07 with 0 mismatches Associated trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb chain B to rhgb07 with 0 mismatches Associated trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb chain C to rhgb07 with 0 mismatches Associated 30B-RBD-only.pdb chain A to rhgb07 with 4 mismatches Associated 8u29 chain A to rhgb07 with 95 mismatches Associated 8u29 chain B to rhgb07 with 95 mismatches Associated 8u29 chain C to rhgb07 with 95 mismatches Associated 8u29 chain A to rhgb07 with 95 mismatches Associated sarscov2closed chain A to cov2 with 1 mismatch Associated sarscov2closed chain B to cov2 with 1 mismatch Associated sarscov2closed chain C to cov2 with 1 mismatch Showing conservation header (""seq_conservation"" residue attribute) for alignment clustalo-I20260401-175019-0503-45788964-p1m.aln Opened 2 sequences from clustalo-I20260401-175019-0503-45788964-p1m.aln > select #13/A-C:336 18 atoms, 15 bonds, 3 residues, 1 model selected > select #13/A-C:336 18 atoms, 15 bonds, 3 residues, 1 model selected > select #13/A-C:336 #1/A-C:327 #4/A:327 #5/A-C:326 #8/A:326 66 atoms, 55 bonds, 11 residues, 5 models selected > select #13/A-C:336 #1/A-C:327 #4/A:327 #5/A-C:326 #8/A:326 66 atoms, 55 bonds, 11 residues, 5 models selected clustalo-I20260401-175019-0503-45788964-p1m.aln [ID: clustalo-I20260401-175019-0503-45788964-p1m.aln] region cov2..rhgb07 [336] RMSD: 1.201 > select #13/A-C:336,361 #1/A-C:327,352 #4/A:327,352 #5/A-C:326,351 > #8/A:326,351 132 atoms, 121 bonds, 22 residues, 5 models selected clustalo-I20260401-175019-0503-45788964-p1m.aln [ID: clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection RMSD: 1.110 > select #13/A-C:336,341,361 #1/A-C:327,332,352 #4/A:327,332,352 > #5/A-C:326,331,351 #8/A:326,331,351 209 atoms, 187 bonds, 33 residues, 5 models selected clustalo-I20260401-175019-0503-45788964-p1m.aln [ID: clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection RMSD: 1.017 > select #13/A-C:336,341-342,361 #1/A-C:327,332-333,352 #4/A:327,332-333,352 > #5/A-C:326,331-332,351 #8/A:326,331-332,351 330 atoms, 319 bonds, 2 pseudobonds, 44 residues, 7 models selected clustalo-I20260401-175019-0503-45788964-p1m.aln [ID: clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection RMSD: 1.017 > select #13/A-C:336,338,341-342,361 #1/A-C:327,329,332-333,352 > #4/A:327,329,332-333,352 #5/A-C:326,328,331-332,351 #8/A:326,328,331-332,351 451 atoms, 440 bonds, 2 pseudobonds, 55 residues, 7 models selected clustalo-I20260401-175019-0503-45788964-p1m.aln [ID: clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection RMSD: 1.058 > select #13/A-C:336,338,341-342,361,374 #1/A-C:327,329,332-333,352,366 > #4/A:327,329,332-333,352,366 #5/A-C:326,328,331-332,351,365 > #8/A:326,328,331-332,351,365 572 atoms, 561 bonds, 2 pseudobonds, 66 residues, 7 models selected clustalo-I20260401-175019-0503-45788964-p1m.aln [ID: clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection RMSD: 1.137 > select #13/A-C:336,338,341-342,361,374,377 > #1/A-C:327,329,332-333,352,366,369 #4/A:327,329,332-333,352,366,369 > #5/A-C:326,328,331-332,351,365,368 #8/A:326,328,331-332,351,365,368 693 atoms, 682 bonds, 2 pseudobonds, 77 residues, 7 models selected clustalo-I20260401-175019-0503-45788964-p1m.aln [ID: clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection RMSD: 1.157 > select #13/A-C:336,338,341-342,361,374,377,392 > #1/A-C:327,329,332-333,352,366,369,384 #4/A:327,329,332-333,352,366,369,384 > #5/A-C:326,328,331-332,351,365,368,383 #8/A:326,328,331-332,351,365,368,383 814 atoms, 803 bonds, 2 pseudobonds, 88 residues, 7 models selected clustalo-I20260401-175019-0503-45788964-p1m.aln [ID: clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection RMSD: 1.159 > select #13/A-C:336,338,341-342,361,374,377,392,515 > #1/A-C:327,329,332-333,352,366,369,384,503 > #4/A:327,329,332-333,352,366,369,384,503 > #5/A-C:326,328,331-332,351,365,368,383,502 > #8/A:326,328,331-332,351,365,368,383,502 923 atoms, 908 bonds, 2 pseudobonds, 99 residues, 7 models selected clustalo-I20260401-175019-0503-45788964-p1m.aln [ID: clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection RMSD: 1.374 > select #13/A-C:336,338,341-342,361,374,377,379,392,515 > #1/A-C:327,329,332-333,352,366,369,371,384,503 > #4/A:327,329,332-333,352,366,369,371,384,503 > #5/A-C:326,328,331-332,351,365,368,370,383,502 > #8/A:326,328,331-332,351,365,368,370,383,502 989 atoms, 963 bonds, 2 pseudobonds, 110 residues, 7 models selected clustalo-I20260401-175019-0503-45788964-p1m.aln [ID: clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection RMSD: 2.012 > select #13/A-C:336,338,341-342,361,374,377,379,392,432,515 > #1/A-C:327,329,332-333,352,366,369,371,384,424,503 > #4/A:327,329,332-333,352,366,369,371,384,424,503 > #5/A-C:326,328,331-332,351,365,368,370,383,423,502 > #8/A:326,328,331-332,351,365,368,370,383,423,502 1055 atoms, 1029 bonds, 2 pseudobonds, 121 residues, 7 models selected clustalo-I20260401-175019-0503-45788964-p1m.aln [ID: clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection RMSD: 1.933 > select #13/A-C:336,338,341-342,361,374,377,379,392,432,436,515 > #1/A-C:327,329,332-333,352,366,369,371,384,424,428,503 > #4/A:327,329,332-333,352,366,369,371,384,424,428,503 > #5/A-C:326,328,331-332,351,365,368,370,383,423,427,502 > #8/A:326,328,331-332,351,365,368,370,383,423,427,502 1209 atoms, 1194 bonds, 2 pseudobonds, 132 residues, 7 models selected clustalo-I20260401-175019-0503-45788964-p1m.aln [ID: clustalo-I20260401-175019-0503-45788964-p1m.aln] region ChimeraX selection RMSD: 1.868 > select #4/A:327,329,332-333,352,366,369,371,384,424,428,503 111 atoms, 110 bonds, 12 residues, 1 model selected > show sel atoms > style sel stick Changed 111 atom styles > ui tool show ""Color Actions"" > color sel #b44e66ff target a > color sel byhetero target a > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > select clear > select #1/A-C:327,329,332-333,352,366,369,371,384,424,428,503 333 atoms, 330 bonds, 36 residues, 1 model selected > show #!4 atoms > hide #!4 atoms > hide #!4 models > show #!1 models > select add #1 27102 atoms, 27867 bonds, 6 pseudobonds, 3399 residues, 2 models selected > select subtract #1 Nothing selected > select #1/A:327,329,332-333,352,366,369,371,384,424,428,503 111 atoms, 110 bonds, 12 residues, 1 model selected > show sel atoms > style sel stick Changed 111 atom styles > color sel #5272aaff target a > color sel #b44e66ff target a > color sel byhetero target a > select #1/B:408-409 11 atoms, 10 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > hide sel atoms > select #1/B:399-400 16 atoms, 15 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 16 atom styles > hide sel atoms > select #1/A-C:400 #4/A:400 #5/A-C:399 #8/A:399 80 atoms, 72 bonds, 8 residues, 4 models selected > select #1/A-C:400-401 #4/A:400-401 #5/A-C:399-400 #8/A:399-400 152 atoms, 144 bonds, 1 pseudobond, 16 residues, 5 models selected clustalo-I20260401-175019-0503-45788964-p1m.aln [ID: clustalo-I20260401-175019-0503-45788964-p1m.aln] region rhgb07 [409-410] RMSD: 0.884 > show sel & #!1 atoms > hide sel & #!1 atoms > select #1/B:400-401 18 atoms, 17 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 18 atom styles > color sel #5272aaff target a > color sel #b44e66ff target a > color sel byhetero target a > select clear > ui tool show ""Side View"" > volume #9.2 level 0.1611 > volume #9.2 level 0.2606 > volume #9.2 level 0.1873 > select add #1/A:356 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 12 atom styles > select clear > select add #1/A:356@CD1 1 atom, 1 residue, 1 model selected > select subtract #1/A:356 Nothing selected > select add #1/A:356 12 atoms, 12 bonds, 1 residue, 1 model selected > ui tool show ""Color Actions"" > color sel #5272aaff target a > color sel #b44e66ff target a > color sel byhetero target a > select clear > volume #9.2 level 0.2475 Drag select of 9.2 103_zflipped.ccp4 1 1 , 3 residues, 1 bonds > select clear Drag select of 1 atoms > select clear > save /Users/kelvinlau/Desktop/image2.png supersample 3 > save /Users/kelvinlau/Desktop/RhGB07-full/v7/rbd-lipid.cxs includeMaps true ===== Log before crash end ===== Log: > graphics silhouettes true > lighting soft > windowsize 800 800 > ui tool hide ""command line interface"" > ui tool show clix UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,4 Model Number: Z15H00063SM/A Chip: Apple M1 Max Total Number of Cores: 10 (8 Performance and 2 Efficiency) Memory: 32 GB System Firmware Version: 13822.81.10 OS Loader Version: 13822.81.10 Software: System Software Overview: System Version: macOS 26.3.1 (a) (25D771280a) Kernel Version: Darwin 25.3.0 Time since boot: 5 days, 18 hours, 31 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 4 Displays: DELL S2722QC: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.5.0 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.18 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-clix: 0.2.5 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 2.5.1 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: 1.6.2 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 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: 1.1.3 ChimeraX-ProfileGrids: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 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: 1.19.1 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: 2.5.2 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: 1.45.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.9.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.4 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.0 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Window Toolkit duplicate all ChimeraX