id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18105 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.7.2-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"" : 240000032 } ], ""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/dario.guerrini/Library/CloudStorage/OneDrive-SharedLibraries- > Htechnopole/Casañal - Documents/DGuerrini/AlphaFold/Ime4-Kar4 > Sup35-Sup45.cxs"" opened ChimeraX session > open ""/Users/dario.guerrini/Library/CloudStorage/OneDrive-SharedLibraries- > Htechnopole/Casañal - Documents/DGuerrini/231115_misky.pdb"" 231115_misky.pdb title: \--- [more info...] Chain information for 231115_misky.pdb #4 --- 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 G | No description available H | No description available I | No description available > hide #1#!4 atoms > show #1#!4 cartoons Computing secondary structure > ui tool show Matchmaker > matchmaker #1-3 to #4 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 231115_misky.pdb, chain A (#4) with fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp_model_0.cif, chain A (#1), sequence alignment score = 1850.1 RMSD between 230 pruned atom pairs is 1.057 angstroms; (across all 439 pairs: 27.748) Matchmaker 231115_misky.pdb, chain A (#4) with fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp_model_1.cif, chain A (#2), sequence alignment score = 1851.8 RMSD between 230 pruned atom pairs is 1.009 angstroms; (across all 439 pairs: 20.993) Matchmaker 231115_misky.pdb, chain A (#4) with fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp_model_2.cif, chain A (#3), sequence alignment score = 1853.7 RMSD between 235 pruned atom pairs is 0.993 angstroms; (across all 439 pairs: 31.793) > color #1#!4 bychain > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > save ""/Users/dario.guerrini/Library/CloudStorage/OneDrive-SharedLibraries- > Htechnopole/Casañal - Documents/DGuerrini/AlphaFold/Ime4-Kar4 > Sup35-Sup45.cxs"" > ui tool show ""AlphaFold Error Plot"" > alphafold pae #3 file > /Users/dario.guerrini/Downloads/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp_full_data_2.json > color #3/D:9-142 lime > color #3/A:160-523 magenta > hide #1 models > show #3 models > hide #3 models > show #2 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #2 file > /Users/dario.guerrini/Downloads/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp_full_data_1.json > color #2/D:6-135 lime > color #2/A:156-519 magenta > hide #2 models > show #1 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file > /Users/dario.guerrini/Downloads/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp_full_data_0.json > color #1/D:10-139 lime > color #1/A:164-519 magenta > show #2 models > hide #1 models > show #1 models > show #3 models > hide #2 models > hide #1 models > hide #3 models > show #3 models > show #3 atoms > hide #3 atoms > interfaces #3 & ~solvent 5 buried areas: A B 4347, C D 2817, A D 1541, D B 773, C E 439 > color #3/D:1-140 lime > color #3/B:39-330 magenta > ui tool show ""Side View"" > lighting soft > graphics silhouettes true > lighting simple > lighting flat > lighting soft > lighting full > lighting simple > graphics silhouettes false > set bgColor gray > set bgColor black > set bgColor white > view > save /Users/dario.guerrini/Desktop/image1.png supersample 3 > select clear > paegreen #3 Unknown command: alphafold paegreen #3 > alphafold pae #3 paegreen Expected a keyword > color #3/D:5-137 lime > color #3/A:164-519 magenta > color #3/D:325 lime > color #3/A:304 magenta > color #3/D:5-143 lime > color #3/A:156-519 magenta > save /Users/dario.guerrini/Desktop/image1.png supersample 3 > ui tool show ""AlphaFold Error Plot"" > alphafold pae #3 file > /Users/dario.guerrini/Downloads/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp/fold_ime4_kar4_nterm_truncated_sup35_sup45_gtp_full_data_2.json > select #/A:160-519 Expected an objects specifier or a keyword > select #/A 160-519 Expected an objects specifier or a keyword > select #3/A:160-519 2911 atoms, 2979 bonds, 360 residues, 1 model selected > ui tool show ""Color Actions"" > color sel orange > select clear > ui mousemode right select > select #3/A:159 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel orange > save /Users/dario.guerrini/Desktop/image1.png supersample 3 > save ""/Users/dario.guerrini/Library/CloudStorage/OneDrive-SharedLibraries- > Htechnopole/Casañal - Documents/DGuerrini/AlphaFold/Ime4-Kar4 > Sup35-Sup45.cxs"" > close session > open ""/Users/dario.guerrini/Library/CloudStorage/OneDrive-SharedLibraries- > Htechnopole/Casañal - > Documents/DGuerrini/AlphaFold/Cap_binding_complex_predictions.cxs"" opened ChimeraX session > open > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_0.cif > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_1.cif > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_2.cif Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_0.cif #22 --- Chain | Description A | . B | . C | . D | . E | . F | . Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_1.cif #23 --- Chain | Description A | . B | . C | . D | . E | . F | . Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_2.cif #24 --- Chain | Description A | . B | . C | . D | . E | . F | . > close #22-24 > close #7-9 > close #1-3 > close #4-6 > close #16-18 > close #19-21 > open > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_0.cif > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_1.cif > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_2.cif Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_0.cif #1 --- Chain | Description A | . B | . C | . D | . E | . F | . Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_1.cif #2 --- Chain | Description A | . B | . C | . D | . E | . F | . Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_2.cif #3 --- Chain | Description A | . B | . C | . D | . E | . F | . > open > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_0.cif > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_1.cif > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_2.cif Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_0.cif #4 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_1.cif #5 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_2.cif #6 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . > open > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_0.cif > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_1.cif > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_2.cif Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_0.cif #7 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_1.cif #8 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . Chain information for fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_2.cif #9 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . > open /Users/dario.guerrini/Library/CloudStorage/OneDrive- > Htechnopole/231115_misky.pdb 231115_misky.pdb title: \--- [more info...] Chain information for 231115_misky.pdb #16 --- 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 G | No description available H | No description available I | No description available > hide #1-9#!16 atoms > show #1-9#!16 cartoons Computing secondary structure > color #1-9#!16 bychain > ui tool show Matchmaker > hide #!16 models > show #!16 models > ui tool show Matchmaker > hide #!16 models > hide #9 models > hide #8 models > hide #7 models > hide #6 models > hide #5 models > hide #4 models > hide #3 models > hide #2 models > hide #1 models > ui tool show Matchmaker > matchmaker #1-15 to #16 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 231115_misky.pdb, chain A (#16) with fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_0.cif, chain A (#1), sequence alignment score = 1862.1 RMSD between 245 pruned atom pairs is 0.998 angstroms; (across all 439 pairs: 19.437) Matchmaker 231115_misky.pdb, chain A (#16) with fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_1.cif, chain A (#2), sequence alignment score = 1845.2 RMSD between 238 pruned atom pairs is 0.989 angstroms; (across all 439 pairs: 23.056) Matchmaker 231115_misky.pdb, chain A (#16) with fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_model_2.cif, chain A (#3), sequence alignment score = 1868.1 RMSD between 236 pruned atom pairs is 1.023 angstroms; (across all 439 pairs: 17.912) Matchmaker 231115_misky.pdb, chain A (#16) with fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_0.cif, chain A (#4), sequence alignment score = 1842.9 RMSD between 241 pruned atom pairs is 1.026 angstroms; (across all 439 pairs: 20.976) Matchmaker 231115_misky.pdb, chain A (#16) with fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_1.cif, chain A (#5), sequence alignment score = 1852.4 RMSD between 248 pruned atom pairs is 0.938 angstroms; (across all 439 pairs: 22.851) Matchmaker 231115_misky.pdb, chain A (#16) with fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_model_2.cif, chain A (#6), sequence alignment score = 1837.5 RMSD between 246 pruned atom pairs is 0.930 angstroms; (across all 439 pairs: 17.769) Matchmaker 231115_misky.pdb, chain A (#16) with fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_0.cif, chain A (#7), sequence alignment score = 1820.7 RMSD between 242 pruned atom pairs is 0.944 angstroms; (across all 439 pairs: 21.197) Matchmaker 231115_misky.pdb, chain A (#16) with fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_1.cif, chain A (#8), sequence alignment score = 1867.5 RMSD between 241 pruned atom pairs is 0.974 angstroms; (across all 439 pairs: 19.413) Matchmaker 231115_misky.pdb, chain A (#16) with fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_model_2.cif, chain A (#9), sequence alignment score = 1860.3 RMSD between 244 pruned atom pairs is 1.007 angstroms; (across all 439 pairs: 24.652) Matchmaker 231115_misky.pdb, chain C (#16) with fold_eif4a_eif4g_eif4e_eif4b_model_0.cif, chain B (#10), sequence alignment score = 225.1 RMSD between 17 pruned atom pairs is 0.666 angstroms; (across all 299 pairs: 28.385) Matchmaker 231115_misky.pdb, chain C (#16) with fold_eif4a_eif4g_eif4e_eif4b_model_1.cif, chain B (#11), sequence alignment score = 241.2 RMSD between 18 pruned atom pairs is 0.768 angstroms; (across all 295 pairs: 32.752) Matchmaker 231115_misky.pdb, chain C (#16) with fold_eif4a_eif4g_eif4e_eif4b_model_2.cif, chain B (#12), sequence alignment score = 226 RMSD between 18 pruned atom pairs is 0.789 angstroms; (across all 297 pairs: 31.804) Matchmaker 231115_misky.pdb, chain D (#16) with fold_eif4a_eif4g_eif4e_eif4b_rec8rna_model_0.cif, chain B (#13), sequence alignment score = 222 RMSD between 10 pruned atom pairs is 1.526 angstroms; (across all 449 pairs: 35.979) Matchmaker 231115_misky.pdb, chain C (#16) with fold_eif4a_eif4g_eif4e_eif4b_rec8rna_model_1.cif, chain B (#14), sequence alignment score = 220.2 RMSD between 18 pruned atom pairs is 0.802 angstroms; (across all 303 pairs: 31.143) Matchmaker 231115_misky.pdb, chain C (#16) with fold_eif4a_eif4g_eif4e_eif4b_rec8rna_model_2.cif, chain B (#15), sequence alignment score = 220.2 RMSD between 14 pruned atom pairs is 0.824 angstroms; (across all 303 pairs: 39.656) > show #!16 models > select clear > ui mousemode right translate > show #1 models > hide #1 models > ui tool show ""Side View"" > hide #!16 models > show #1 models > hide #1 models > show #10 models > hide #10 models > show #!16 models > select #16/A:160-519 2511 atoms, 2566 bonds, 4 pseudobonds, 308 residues, 2 models selected > select clear > show #1 models > hide #1 models > show #1 models > hide #!16 models > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_full_data_0.json > color #1/F:365-371 lime > color #1/B:35-47 magenta > color #1/F:371-398 lime > color #1/B:29-320 magenta > hide #1 models > show #4 models > ui mousemode right pivot > ui mousemode right translate > ui tool show ""AlphaFold Error Plot"" > alphafold pae #4 file > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_nocap_full_data_0.json > color #4/D:568-917 lime > color #4/B:35-329 magenta > color #4/D:860-886 lime > color #4/B:47-335/C:1-6 magenta > color #4/G:11-24 lime > color #4/B:40-335/C:1-2 magenta > color #4/D:859-894 lime > color #4/A:182-600/B:1-331 magenta > color #4/D:566 lime > color #4/B:140 magenta > color #4/D:863-890 lime > color #4/A:182-524 magenta > select #4/G 605 atoms, 678 bonds, 28 residues, 1 model selected > color sel cyan > select #4/A:187-524 2731 atoms, 2797 bonds, 338 residues, 1 model selected > color sel orange > ui mousemode right select > select #4/A:183 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #4/A:182 16 atoms, 14 bonds, 2 residues, 1 model selected > select add #4/A:184 25 atoms, 22 bonds, 3 residues, 1 model selected > select add #4/A:186 32 atoms, 28 bonds, 4 residues, 1 model selected > select add #4/A:185 44 atoms, 40 bonds, 5 residues, 1 model selected > color sel orange > hide #4 models > show #4 models > hide #4 models > show #1 models > hide #1 models > show #7 models > hide #7 models > show #4 models > hide #4 models > show #7 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #7 file > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_rec8proberna_full_data_0.json > color #7/E:36-213 lime > color #7/A:178-511 magenta Drag select of 9 residues > undo > ui mousemode right translate > select clear > color #7 bychain > select #7/E:58 14 atoms, 15 bonds, 1 residue, 1 model selected > 104 Unknown command: 104 > select #7/E:58-104 408 atoms, 424 bonds, 47 residues, 1 model selected > ui mousemode right pivot > ui mousemode right translate > ui mousemode right select > select #7/E:104 14 atoms, 15 bonds, 1 residue, 1 model selected > select add #7/E:58 28 atoms, 30 bonds, 2 residues, 1 model selected > show sel atoms > hide sel surfaces > hide sel atoms > show sel atoms > style sel stick Changed 28 atom styles > color sel red > ui mousemode right translate > select #7/G 606 atoms, 679 bonds, 28 residues, 1 model selected > color sel cyan > select #7/G:1 25 atoms, 27 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 25 atom styles > lighting soft > lighting flat > select clear > save /Users/dario.guerrini/Desktop/image1.png supersample 3 > hide #7 models > show #1 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file > /Users/dario.guerrini/Downloads/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b/fold_ime4_kar4_eif4a_eif4g_eif4e_eif4b_full_data_0.json > ui mousemode right pivot > ui mousemode right translate > save /Users/dario.guerrini/Desktop/image1.png supersample 3 > hide #1 models > show #4 models > save /Users/dario.guerrini/Desktop/image1.png supersample 3 > color #7/B:327 lime > color #7/D:734 magenta > color #4/C:68-164 lime > color #4/A:177-524 magenta > select #4/G 605 atoms, 678 bonds, 28 residues, 1 model selected > color sel cyan > select #4/A:182-523 2766 atoms, 2833 bonds, 342 residues, 1 model selected > color sel orange > select clear > ui mousemode right select > select #4/A:179 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/A:181 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/A:180 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #4/A:181 18 atoms, 16 bonds, 2 residues, 1 model selected > select add #4/A:179 23 atoms, 20 bonds, 3 residues, 1 model selected > select subtract #4/A:179 18 atoms, 16 bonds, 2 residues, 1 model selected > select add #4/A:524 27 atoms, 24 bonds, 3 residues, 1 model selected > color sel orange > select #4/A:179 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #4/A:178 13 atoms, 11 bonds, 2 residues, 1 model selected > color sel orange Drag select of 6 residues > select clear > ui mousemode right translate > select clear > color #4 bychain > select #4/G 605 atoms, 678 bonds, 28 residues, 1 model selected > color sel cyan > select clear > select #4/G 605 atoms, 678 bonds, 28 residues, 1 model selected > select #4/G 605 atoms, 678 bonds, 28 residues, 1 model selected > select #4/G zr select sel : show sel > hide ~sel > select ~sel & ##selected 301817 atoms, 308352 bonds, 34 pseudobonds, 37680 residues, 16 models selected > hide sel & #4 cartoons > undo > select ~sel & ##selected 12751 atoms, 12876 bonds, 1348 residues, 15 models selected > select clear > select #4/G 605 atoms, 678 bonds, 28 residues, 1 model selected > select sel : select sel : select ~sel & ##selected 236993 atoms, 242530 bonds, 30 pseudobonds, 29735 residues, 17 models selected > hide sel & #4 cartoons > select #4/G:1 24 atoms, 26 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 24 atom styles > select clear > select #4/E:58 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 14 atom styles > color sel red > select #4/E:104 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 14 atom styles > color sel red > save /Users/dario.guerrini/Desktop/image1.png supersample 3 > hide #4 models > show #1 models > show #7 models > hide #1 models > color #7 bychain > select #7/G 606 atoms, 679 bonds, 28 residues, 1 model selected > color sel cyan > select sel : select ~sel & ##selected 284223 atoms, 290558 bonds, 34 pseudobonds, 35505 residues, 16 models selected > hide sel & #7 cartoons > undo > select #7/G 606 atoms, 679 bonds, 28 residues, 1 model selected > select sel : select sel : select ~sel & ##selected 199921 atoms, 204652 bonds, 27 pseudobonds, 25043 residues, 17 models selected > hide sel & #7 cartoons > select #7/G:1 25 atoms, 27 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 25 atom styles > select #7/E:58 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > select #7/E:104 14 atoms, 15 bonds, 1 residue, 1 model selected > color sel red > show sel atoms > style sel stick Changed 14 atom styles > save /Users/dario.guerrini/Desktop/image1.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 - 88.1 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: Z1B8001FCT/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.140.19.700.2 OS Loader Version: 10151.140.19.700.2 Software: System Software Overview: System Version: macOS 14.7.2 (23H311) Kernel Version: Darwin 23.6.0 Time since boot: 35 days, 21 hours, 26 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 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