id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17144 Crash on Mac waking from sleep halle.andrews-clark@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.0.1-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. 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""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_0.cif"" > ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S > rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_1.cif"" > ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S > rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_2.cif"" > ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S > rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_3.cif"" > ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S > rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_4.cif"" Chain information for fold_snd1_ribs_exit_interact_model_0.cif #1 --- Chain | Description A | . B | . C | . D | . E | . Chain information for fold_snd1_ribs_exit_interact_model_1.cif #2 --- Chain | Description A | . B | . C | . D | . E | . Chain information for fold_snd1_ribs_exit_interact_model_2.cif #3 --- Chain | Description A | . B | . C | . D | . E | . Chain information for fold_snd1_ribs_exit_interact_model_3.cif #4 --- Chain | Description A | . B | . C | . D | . E | . Chain information for fold_snd1_ribs_exit_interact_model_4.cif #5 --- Chain | Description A | . B | . C | . D | . E | . > select 413705 atoms, 457795 bonds, 23350 residues, 5 models selected > cartoon sel > hide sel target a > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /20250221_scSND1-ribosome.cxs"" Opened cryosparc_P26_J86_005_volume_map.mrc as #1, grid size 320,320,320, pixel 1.34, shown at level 0.3, step 1, values float32 Opened emdb 16191 as #5, grid size 420,420,420, pixel 1.08, shown at level 0.0247, step 2, values float32 opened ChimeraX session > hide #!1 models > hide #2 models > hide #3 models > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_0.cif"" Chain information for fold_snd1_ribs_exit_interact_model_0.cif #7 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_1.cif"" Chain information for fold_snd1_ribs_exit_interact_model_1.cif #8 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_2.cif"" Chain information for fold_snd1_ribs_exit_interact_model_2.cif #9 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_3.cif"" Chain information for fold_snd1_ribs_exit_interact_model_3.cif #10 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_4.cif"" Chain information for fold_snd1_ribs_exit_interact_model_4.cif #11 --- Chain | Description A | . B | . C | . D | . E | . > hide #7 models > show #7 models > select add #7 82741 atoms, 91559 bonds, 4670 residues, 1 model selected > select add #8 165482 atoms, 183118 bonds, 9340 residues, 2 models selected > select add #9 248223 atoms, 274677 bonds, 14010 residues, 3 models selected > select add #10 330964 atoms, 366236 bonds, 18680 residues, 4 models selected > select add #11 413705 atoms, 457795 bonds, 23350 residues, 5 models selected > hide sel target a > cartoon sel > show #3 models > show #2 models > show #!4 models > select clear > ui tool show Matchmaker > matchmaker #7 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 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_0.cif, chain E (#7), sequence alignment score = 19589.3 RMSD between 2794 pruned atom pairs is 0.843 angstroms; (across all 3301 pairs: 9.094) > ui tool show Matchmaker > matchmaker #8 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 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_1.cif, chain E (#8), sequence alignment score = 19589.3 RMSD between 2734 pruned atom pairs is 0.939 angstroms; (across all 3301 pairs: 8.192) > ui tool show Matchmaker > matchmaker #9 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 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_2.cif, chain E (#9), sequence alignment score = 19589.3 RMSD between 2703 pruned atom pairs is 0.914 angstroms; (across all 3301 pairs: 6.995) > ui tool show Matchmaker > matchmaker #10 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 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_3.cif, chain E (#10), sequence alignment score = 19589.3 RMSD between 2720 pruned atom pairs is 0.870 angstroms; (across all 3301 pairs: 9.636) > ui tool show Matchmaker > matchmaker #11 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 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_4.cif, chain E (#11), sequence alignment score = 19589.3 RMSD between 2737 pruned atom pairs is 0.854 angstroms; (across all 3301 pairs: 8.399) > select add #7 82741 atoms, 91559 bonds, 4670 residues, 1 model selected > select add #8 165482 atoms, 183118 bonds, 9340 residues, 2 models selected > select add #9 248223 atoms, 274677 bonds, 14010 residues, 3 models selected > select add #10 330964 atoms, 366236 bonds, 18680 residues, 4 models selected > select add #11 413705 atoms, 457795 bonds, 23350 residues, 5 models selected > cartoon sel > hide #!4 models > show #!4 models > save ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /exit tunnel /exit tunnel AF3 snd1.cxs"" > cartoon sel > select add #2 416078 atoms, 460209 bonds, 23646 residues, 6 models selected > select subtract #2 413705 atoms, 457795 bonds, 23350 residues, 5 models selected > close session > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /exit tunnel /exit tunnel AF3 snd1.cxs"" format session Opened cryosparc_P26_J86_005_volume_map.mrc as #1, grid size 320,320,320, pixel 1.34, shown at level 0.3, step 1, values float32 Opened emdb 16191 as #5, grid size 420,420,420, pixel 1.08, shown at level 0.0247, step 2, values float32 opened ChimeraX session > select add #1 413705 atoms, 457795 bonds, 23350 residues, 7 models selected > select subtract #1 413705 atoms, 457795 bonds, 23350 residues, 5 models selected > show #!1 models > hide #!1 models > cartoon sel > show sel target ab > close session > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_0.cif"" > ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S > rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_1.cif"" > ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S > rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_2.cif"" > ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S > rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_3.cif"" > ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with 25S > rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_4.cif"" Chain information for fold_snd1_ribs_exit_interact_model_0.cif #1 --- Chain | Description A | . B | . C | . D | . E | . Chain information for fold_snd1_ribs_exit_interact_model_1.cif #2 --- Chain | Description A | . B | . C | . D | . E | . Chain information for fold_snd1_ribs_exit_interact_model_2.cif #3 --- Chain | Description A | . B | . C | . D | . E | . Chain information for fold_snd1_ribs_exit_interact_model_3.cif #4 --- Chain | Description A | . B | . C | . D | . E | . Chain information for fold_snd1_ribs_exit_interact_model_4.cif #5 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /20250221_scSND1-ribosome.cxs"" Opened cryosparc_P26_J86_005_volume_map.mrc as #1, grid size 320,320,320, pixel 1.34, shown at level 0.3, step 1, values float32 Opened emdb 16191 as #5, grid size 420,420,420, pixel 1.08, shown at level 0.0247, step 2, values float32 opened ChimeraX session > hide #!1 models > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_0.cif"" Chain information for fold_snd1_ribs_exit_interact_model_0.cif #7 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_1.cif"" Chain information for fold_snd1_ribs_exit_interact_model_1.cif #8 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_2.cif"" Chain information for fold_snd1_ribs_exit_interact_model_2.cif #9 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_3.cif"" Chain information for fold_snd1_ribs_exit_interact_model_3.cif #10 --- Chain | Description A | . B | . C | . D | . E | . > open ""/Users/haandrew/Documents/progress/2025/RNA modelling/modelling with > 25S rRNA /exit tunnel > /fold_snd1_ribs_exit_interact/fold_snd1_ribs_exit_interact_model_4.cif"" Chain information for fold_snd1_ribs_exit_interact_model_4.cif #11 --- Chain | Description A | . B | . C | . D | . E | . > ui tool show Matchmaker > matchmaker #7 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 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_0.cif, chain E (#7), sequence alignment score = 19589.3 RMSD between 2794 pruned atom pairs is 0.843 angstroms; (across all 3301 pairs: 9.094) > ui tool show Matchmaker > matchmaker #8 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 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_1.cif, chain E (#8), sequence alignment score = 19589.3 RMSD between 2734 pruned atom pairs is 0.939 angstroms; (across all 3301 pairs: 8.192) > ui tool show Matchmaker > matchmaker #9 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 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_2.cif, chain E (#9), sequence alignment score = 19589.3 RMSD between 2703 pruned atom pairs is 0.914 angstroms; (across all 3301 pairs: 6.995) > ui tool show Matchmaker > matchmaker #10 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 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_3.cif, chain E (#10), sequence alignment score = 19589.3 RMSD between 2720 pruned atom pairs is 0.870 angstroms; (across all 3301 pairs: 9.636) > ui tool show Matchmaker > matchmaker #11 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 8bqx, chain BQ (#4) with fold_snd1_ribs_exit_interact_model_4.cif, chain E (#11), sequence alignment score = 19589.3 RMSD between 2737 pruned atom pairs is 0.854 angstroms; (across all 3301 pairs: 8.399) > show #!4 models > hide #!4 models > select add #7 82741 atoms, 91559 bonds, 4670 residues, 1 model selected > select add #8 165482 atoms, 183118 bonds, 9340 residues, 2 models selected > select add #9 248223 atoms, 274677 bonds, 14010 residues, 3 models selected > select add #10 330964 atoms, 366236 bonds, 18680 residues, 4 models selected > select add #11 413705 atoms, 457795 bonds, 23350 residues, 5 models selected > cartoon sel > hide sel target a > select subtract #7 330964 atoms, 366236 bonds, 18680 residues, 4 models selected > select subtract #8 248223 atoms, 274677 bonds, 14010 residues, 3 models selected > select subtract #9 165482 atoms, 183118 bonds, 9340 residues, 2 models selected > select subtract #10 82741 atoms, 91559 bonds, 4670 residues, 1 model selected > select subtract #11 Nothing selected > hide #2 models > select add #7 82741 atoms, 91559 bonds, 4670 residues, 1 model selected > select add #8 165482 atoms, 183118 bonds, 9340 residues, 2 models selected > select add #9 248223 atoms, 274677 bonds, 14010 residues, 3 models selected > select add #10 330964 atoms, 366236 bonds, 18680 residues, 4 models selected > select add #11 413705 atoms, 457795 bonds, 23350 residues, 5 models selected > color sel dim gray > select subtract #7 330964 atoms, 366236 bonds, 18680 residues, 4 models selected > select subtract #8 248223 atoms, 274677 bonds, 14010 residues, 3 models selected > select subtract #9 165482 atoms, 183118 bonds, 9340 residues, 2 models selected > select subtract #10 82741 atoms, 91559 bonds, 4670 residues, 1 model selected > select subtract #11 Nothing selected > select #7/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > color sel red > select #8/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select #8/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > color sel red > select #9/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > color sel red > select #10/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > color sel red > select #11/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > color sel red > select clear > select #10/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select #11/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select #10/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select #9/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select ~sel 743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 18 models selected > select subtract #1 743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 16 models selected > select subtract #2 741048 atoms, 810222 bonds, 8431 pseudobonds, 49736 residues, 15 models selected > select subtract #3 738675 atoms, 807808 bonds, 8431 pseudobonds, 49440 residues, 14 models selected > select subtract #4 535766 atoms, 589798 bonds, 3276 pseudobonds, 32738 residues, 10 models selected > select subtract #5 535766 atoms, 589798 bonds, 3276 pseudobonds, 32738 residues, 8 models selected > select subtract #6 406791 atoms, 450766 bonds, 22473 residues, 5 models selected > select subtract #7 324050 atoms, 359207 bonds, 17803 residues, 4 models selected > select subtract #8 241309 atoms, 267648 bonds, 13133 residues, 3 models selected > select add #9 248223 atoms, 274677 bonds, 14010 residues, 3 models selected > select subtract #10 165482 atoms, 183118 bonds, 9340 residues, 2 models selected > select subtract #11 82741 atoms, 91559 bonds, 4670 residues, 1 model selected > select subtract #9 Nothing selected > select add #7 82741 atoms, 91559 bonds, 4670 residues, 1 model selected > select #7/B:1-188 1522 atoms, 1539 bonds, 188 residues, 1 model selected > select #7/C:1-109 891 atoms, 905 bonds, 109 residues, 1 model selected > hide #3 models > hide #8 models > hide #9 models > hide #10 models > hide #11 models > select add #7 82741 atoms, 91559 bonds, 4670 residues, 1 model selected > select subtract #7 Nothing selected > select #7/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select ~sel 743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 18 models selected > cartoon hide (#7 & sel) > hide #7 models > show #8 models > select #8/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select ~sel 743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 18 models selected > cartoon hide (#8 & sel) > hide #8 models > show #9 models > select #9/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select ~sel 743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 18 models selected > cartoon hide (#9 & sel) > hide #9 models > show #10 models > select #10/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select ~sel 743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 18 models selected > cartoon hide (#10 & sel) > hide #10 models > show #11 models > select #11/A:1-877 6914 atoms, 7029 bonds, 877 residues, 1 model selected > select ~sel 743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 18 models selected > cartoon hide (#11 & sel) > show #10 models > show #9 models > show #8 models > show #7 models > show #3 models > color #3 white > color #3 #0100f5ff > select subtract #1 743421 atoms, 812636 bonds, 8431 pseudobonds, 50032 residues, 16 models selected > select subtract #2 741048 atoms, 810222 bonds, 8431 pseudobonds, 49736 residues, 15 models selected > select subtract #3 738675 atoms, 807808 bonds, 8431 pseudobonds, 49440 residues, 14 models selected > select subtract #4 535766 atoms, 589798 bonds, 3276 pseudobonds, 32738 residues, 10 models selected > select subtract #5 535766 atoms, 589798 bonds, 3276 pseudobonds, 32738 residues, 8 models selected > select subtract #6 406791 atoms, 450766 bonds, 22473 residues, 5 models selected > select subtract #7 324050 atoms, 359207 bonds, 17803 residues, 4 models selected > select subtract #8 241309 atoms, 267648 bonds, 13133 residues, 3 models selected > select subtract #9 158568 atoms, 176089 bonds, 8463 residues, 2 models selected > select subtract #10 75827 atoms, 84530 bonds, 3793 residues, 1 model selected > select add #11 82741 atoms, 91559 bonds, 4670 residues, 1 model selected > select subtract #11 Nothing selected > show #!4 models > color #4 #4a4a4aff > show #2 models > hide #2 models > save /Users/haandrew/Desktop/image36.png supersample 3 > save /Users/haandrew/Desktop/image37.png supersample 3 > save /Users/haandrew/Desktop/image38.png supersample 3 > show #2 models > save /Users/haandrew/Desktop/image39.png supersample 3 > ui tool show ""Side View"" > hide #7 models > show #7 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > show #10 models > hide #11 models > save /Users/haandrew/Desktop/image40.png supersample 3 > ui tool show ""Side View"" > hide #2 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: Z11D000L9D/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8419.41.10 OS Loader Version: 8419.41.10 Software: System Software Overview: System Version: macOS 13.0.1 (22A400) Kernel Version: Darwin 22.1.0 Time since boot: 5 days, 3 hours, 2 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX