id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17768 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x000000032d493000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032c487000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032b47b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File 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recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031bcb3000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031aca7000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000319c9b000 (most 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""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000317c83000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000202308840 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, 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""arch"" : ""arm64e"", ""base"" : 6874419200, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.Foundation"", ""size"" : 14974976, ""uuid"" : ""16d282d0-8b48-3e76-8036-fcb45dece518"", ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""3302.1.400"" } ], ""sharedCache"" : { ""base"" : 6850658304, ""size"" : 4865835008, ""uuid"" : ""d272b91e-f9f0-3854-b5b9-508b21c25dcc"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=3.3G written=1976K(0%) resident=1976K(0%) swapped_out=0K(0%) unallocated=3.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 1312K 61 \nColorSync 656K 33 \nCoreAnimation 3248K 195 \nCoreGraphics 80K 5 \nCoreUI image data 5440K 49 \nFoundation 48K 2 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""rolloutId"" : ""64b21a7351cbb02ce3442e4e"", ""factorPackIds"" : { ""REMINDERS_GROCERY"" : ""6647f0f7b6a75d3dc32993e7"" }, ""deploymentId"" : 240000042 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000470 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields still retrieving bundle list from toolshed > isolde shorthand Error running startup command 'isolde shorthand': Unknown command: isolde shorthand 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 ""/Volumes/FS/Common/RAT project/_pMHC > alphafold/pnawrath/E1_20/outputs/9/structure_model_1_9.pdb"" Chain information for structure_model_1_9.pdb #1 --- Chain | Description M | No description available P | No description available Computing secondary structure > open ""/Volumes/FS/Common/RAT project/_pMHC > alphafold/pnawrath/E1_20/outputs/9/structure_model_1_0.pdb"" Chain information for structure_model_1_0.pdb #2 --- Chain | Description M | No description available P | No description available > open ""/Volumes/FS/Common/RAT project/_pMHC > alphafold/pnawrath/E1_20/outputs/9/structure_model_1_1.pdb"" Chain information for structure_model_1_1.pdb #3 --- Chain | Description M | No description available P | No description available > open ""/Volumes/FS/Common/RAT project/_pMHC > alphafold/pnawrath/E1_20/outputs/9/structure_model_1_2.pdb"" Chain information for structure_model_1_2.pdb #4 --- Chain | Description M | No description available P | No description available > open ""/Volumes/FS/Common/RAT project/_pMHC > alphafold/pnawrath/E1_20/outputs/9/structure_model_1_3.pdb"" Chain information for structure_model_1_3.pdb #5 --- Chain | Description M | No description available P | No description available > open ""/Volumes/FS/Common/RAT project/_pMHC > alphafold/pnawrath/E1_20/outputs/9/structure_model_1_4.pdb"" Chain information for structure_model_1_4.pdb #6 --- Chain | Description M | No description available P | No description available > open ""/Volumes/FS/Common/RAT project/_pMHC > alphafold/pnawrath/E1_20/outputs/9/structure_model_1_5.pdb"" Chain information for structure_model_1_5.pdb #7 --- Chain | Description M | No description available P | No description available > open ""/Volumes/FS/Common/RAT project/_pMHC > alphafold/pnawrath/E1_20/outputs/9/structure_model_1_6.pdb"" Chain information for structure_model_1_6.pdb #8 --- Chain | Description M | No description available P | No description available > open ""/Volumes/FS/Common/RAT project/_pMHC > alphafold/pnawrath/E1_20/outputs/9/structure_model_1_7.pdb"" Chain information for structure_model_1_7.pdb #9 --- Chain | Description M | No description available P | No description available > open ""/Volumes/FS/Common/RAT project/_pMHC > alphafold/pnawrath/E1_20/outputs/9/structure_model_1_8.pdb"" Chain information for structure_model_1_8.pdb #10 --- Chain | Description M | No description available P | No description available Computing secondary structure > ui tool show Matchmaker > matchmaker #2-10 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_0.pdb, chain M (#2), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.233 angstroms; (across all 182 pairs: 0.233) Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_1.pdb, chain M (#3), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.210 angstroms; (across all 182 pairs: 0.210) Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_2.pdb, chain M (#4), sequence alignment score = 980.3 RMSD between 182 pruned atom pairs is 0.198 angstroms; (across all 182 pairs: 0.198) Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_3.pdb, chain M (#5), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.169 angstroms; (across all 182 pairs: 0.169) Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_4.pdb, chain M (#6), sequence alignment score = 980.3 RMSD between 182 pruned atom pairs is 0.088 angstroms; (across all 182 pairs: 0.088) Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_5.pdb, chain M (#7), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.226 angstroms; (across all 182 pairs: 0.226) Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_6.pdb, chain M (#8), sequence alignment score = 980.3 RMSD between 181 pruned atom pairs is 0.262 angstroms; (across all 182 pairs: 0.363) Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_7.pdb, chain M (#9), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.181 angstroms; (across all 182 pairs: 0.181) Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_8.pdb, chain M (#10), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.148 angstroms; (across all 182 pairs: 0.148) > select #1/M#2/M#3/M#4/M#5/M#6/M#7/M#8/M#9/M#10/M 14960 atoms, 15320 bonds, 1820 residues, 10 models selected > hide sel atoms > hide sel cartoons > select #1/M 1496 atoms, 1532 bonds, 182 residues, 1 model selected > select #6/M 1496 atoms, 1532 bonds, 182 residues, 1 model selected > show sel cartoons > color #6 #d3d3d344 > set bgColor white > color #6 #d3d3d35e > select #1/P#2/P#3/P#4/P#5/P#6/P#7/P#8/P#9/P#10/P 920 atoms, 950 bonds, 100 residues, 10 models selected > hide sel cartoons > show sel atoms > hide #1 models > hide #2 models > hide #3 models > hide #4 models > hide #6 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > show #6 models > select clear > show #1 models > hide #5 models > show #5 models > hide #1 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #1 models > color bfactor palette alphafold 15880 atoms, 1920 residues, atom bfactor range 49.3 to 98.9 > select add #1 1588 atoms, 1627 bonds, 192 residues, 1 model selected > color bfactor palette alphafold 15880 atoms, 1920 residues, atom bfactor range 49.3 to 98.9 > color #6 #d6d6d6ff > color #6 #d6d6d631 > color #6 #d6d6d630 > hide #6 models > show #6 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > undo > color bfactor palette alphafold 15880 atoms, 1920 residues, atom bfactor range 49.3 to 98.9 > select clear > show #5 models > hide #1 models > show #1 models > hide #1 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #3 models > hide #3 models > show #4 models > hide #4 models > show #7 models > hide #7 models > show #7 models > hide #7 models > show #7 models > hide #5 models > show #5 models > hide #5 models > show #5 models > show #1 models > hide #1 models > hide #5 models > hide #6 models > show #6 models > hide #7 models > show #5 models > show #7 models > hide #7 models > show #8 models > hide #8 models > show #9 models > hide #9 models > show #9 models > hide #9 models > show #10 models > hide #10 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #9 models > hide #9 models > show #8 models > hide #8 models > show #7 models > hide #5 models > hide #7 models > show #5 models > hide #6 models > show #6 models > hide #5 models > close #1-5 > close #7-10 > rename #6 mhc > select /P 92 atoms, 95 bonds, 10 residues, 1 model selected > delete atoms sel > delete bonds sel > select /M 1496 atoms, 1532 bonds, 182 residues, 1 model selected > set bgColor black > select clear > set bgColor white > set bgColor black > set bgColor white > open > /Users/philippnawrath/Desktop/alphafold/results/MOG_peps/MOG_peps/outputs/0/structure_model_1_12.pdb Chain information for structure_model_1_12.pdb #1 --- Chain | Description M | No description available P | No description available Computing secondary structure > open > /Users/philippnawrath/Desktop/alphafold/results/MOG_peps/MOG_peps/outputs/1/structure_model_1_4.pdb Chain information for structure_model_1_4.pdb #2 --- Chain | Description M | No description available P | No description available Computing secondary structure > open > /Users/philippnawrath/Desktop/alphafold/results/MOG_peps/MOG_peps/outputs/2/structure_model_1_0.pdb Chain information for structure_model_1_0.pdb #3 --- Chain | Description M | No description available P | No description available Computing secondary structure > matchmaker #1-3 to #6 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 mhc, chain M (#6) with structure_model_1_12.pdb, chain M (#1), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.187 angstroms; (across all 182 pairs: 0.187) Matchmaker mhc, chain M (#6) with structure_model_1_4.pdb, chain M (#2), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.168 angstroms; (across all 182 pairs: 0.168) Matchmaker mhc, chain M (#6) with structure_model_1_0.pdb, chain M (#3), sequence alignment score = 977.3 RMSD between 181 pruned atom pairs is 0.209 angstroms; (across all 182 pairs: 0.310) > open ""/Volumes/FS/Common/RAT project/_pMHC > alphafold/pnawrath/E1_20/outputs/9/structure_model_1_5.pdb"" Chain information for structure_model_1_5.pdb #4 --- Chain | Description M | No description available P | No description available Computing secondary structure > rename #4 RPPIFIRRLH > rename #1 MASLSRPSLP > rename #2 LSRPSLPSCL > rename #3 KVTLRIRNVR > open ""/Volumes/FS/Common/RAT project/_pMHC > alphafold/pnawrath/E21_40/outputs/21/structure_model_1_9.pdb"" Chain information for structure_model_1_9.pdb #5 --- Chain | Description M | No description available P | No description available Computing secondary structure > rename #5 APHTPLPPVS > rename #5 ""APHTPLPPVS (1-B09)"" > rename #4 ""RPPIFIRRLH (1-A09)"" > rename #3 ""KVTLRIRNVR MOG109_118"" > rename #1 ""MASLSRPSLP MOG1_10"" > rename #2 ""LSRPSLPSCL (MOG4_13)"" > rename #1 ""MASLSRPSLP (MOG1_10)"" > rename #3 ""KVTLRIRNVR (MOG109_118)"" > matchmaker #1-5 to #6 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 mhc, chain M (#6) with MASLSRPSLP (MOG1_10), chain M (#1), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.187 angstroms; (across all 182 pairs: 0.187) Matchmaker mhc, chain M (#6) with LSRPSLPSCL (MOG4_13), chain M (#2), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.168 angstroms; (across all 182 pairs: 0.168) Matchmaker mhc, chain M (#6) with KVTLRIRNVR (MOG109_118), chain M (#3), sequence alignment score = 977.3 RMSD between 181 pruned atom pairs is 0.209 angstroms; (across all 182 pairs: 0.310) Matchmaker mhc, chain M (#6) with RPPIFIRRLH (1-A09), chain M (#4), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.237 angstroms; (across all 182 pairs: 0.237) Matchmaker mhc, chain M (#6) with APHTPLPPVS (1-B09), chain M (#5), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.121 angstroms; (across all 182 pairs: 0.121) > select #1/P#2/P#3/P#4/P#5/P 395 atoms, 403 bonds, 50 residues, 5 models selected > select #1/M#2/M#3/M#4/M#5/M#6/M 8976 atoms, 9192 bonds, 1092 residues, 6 models selected > hide sel atoms > hide sel cartoons > select #6/M 1496 atoms, 1532 bonds, 182 residues, 1 model selected > show sel cartoons > select #1/P#2/P#3/P#4/P#5/P 395 atoms, 403 bonds, 50 residues, 5 models selected > hide sel cartoons > show sel atoms > select clear > hide #1 models > hide #2 models > hide #5 models > hide #4 models > show #5 models > hide #3 models > show #2 models > hide #2 models > show #1 models > hide #1 models > show #2 models > hide #2 models > show #3 models > hide #5 models > show #4 models > open ""/Volumes/FS/Common/RAT project/_pMHC > alphafold/pnawrath/E1_20/outputs/8/structure_model_1_4.pdb"" Chain information for structure_model_1_4.pdb #7 --- Chain | Description M | No description available P | No description available Computing secondary structure > open ""/Volumes/FS/Common/RAT project/_pMHC > alphafold/pnawrath/E1_20/outputs/10/structure_model_1_3.pdb"" Chain information for structure_model_1_3.pdb #8 --- Chain | Description M | No description available P | No description available Computing secondary structure > matchmaker #1-5,7-8 to #6 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 mhc, chain M (#6) with MASLSRPSLP (MOG1_10), chain M (#1), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.187 angstroms; (across all 182 pairs: 0.187) Matchmaker mhc, chain M (#6) with LSRPSLPSCL (MOG4_13), chain M (#2), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.168 angstroms; (across all 182 pairs: 0.168) Matchmaker mhc, chain M (#6) with KVTLRIRNVR (MOG109_118), chain M (#3), sequence alignment score = 977.3 RMSD between 181 pruned atom pairs is 0.209 angstroms; (across all 182 pairs: 0.310) Matchmaker mhc, chain M (#6) with RPPIFIRRLH (1-A09), chain M (#4), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.237 angstroms; (across all 182 pairs: 0.237) Matchmaker mhc, chain M (#6) with APHTPLPPVS (1-B09), chain M (#5), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.121 angstroms; (across all 182 pairs: 0.121) Matchmaker mhc, chain M (#6) with structure_model_1_4.pdb, chain M (#7), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.121 angstroms; (across all 182 pairs: 0.121) Matchmaker mhc, chain M (#6) with structure_model_1_3.pdb, chain M (#8), sequence alignment score = 977.3 RMSD between 182 pruned atom pairs is 0.172 angstroms; (across all 182 pairs: 0.172) > select #1/M#2/M#3/M#4/M#5/M#6/M#7/M#8/M 11968 atoms, 12256 bonds, 1456 residues, 8 models selected > hide sel & #3-4,6-8 cartoons > hide sel & #3-4,6-8 atoms > select #6/M 1496 atoms, 1532 bonds, 182 residues, 1 model selected > show sel cartoons > rename #7 ""KPTPPPSRR (1-A08)"" > rename #8 ""TPTPPPQVP (A-A10)"" > hide #4 models > select clear > hide #3 models > hide #8 models > show #4 models > hide #4 models > show #5 models > hide #5 models > show #3 models > show #5 models > hide #7 models > hide #3 models > show #4 models > hide #5 models > select #4/P 92 atoms, 95 bonds, 10 residues, 1 model selected > label sel attribute name > label sel attribute label_specifier > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select clear > color #4 #ff2600ff > undo > color #4 #797979ff > color #4 #212121ff > color #4 #9437ffff > color #4 #00fdffff > color #4 #d99090ff > select #4/P 92 atoms, 95 bonds, 10 residues, 1 model selected > color sel byhetero > select clear > save /Users/philippnawrath/Desktop/image1.png supersample 3 > labelopt bold true Unknown command: labelopt bold true > label text @/name style bold Expected a keyword > select #4/P 92 atoms, 95 bonds, 10 residues, 1 model selected > label sel text @/name style bold Expected a keyword > open 6VMX 6vmx title: Structure of HD14 TCR in complex with HLA-B7 presenting an EBV epitope [more info...] Chain information for 6vmx #9 --- Chain | Description | UniProt A F | HLA class I histocompatibility antigen, B-7 alpha chain | 1B07_HUMAN 1-276 B G | Beta-2-microglobulin | B2MG_HUMAN 1-99 C H | Epstein-Barr nuclear antigen 3 | EBNA3_EBVB9 1-9 D I | HD14 alpha chain | E J | HD14 beta chain | Non-standard residues in 6vmx #9 --- EDO — 1,2-ethanediol (ethylene glycol) PEG — di(hydroxyethyl)ether 6vmx mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 53 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!4 models > hide #6 models > select add #9 13603 atoms, 13843 bonds, 1 pseudobond, 1795 residues, 3 models selected > hide sel & #!9 atoms > show sel & #!9 cartoons > select #9/B 842 atoms, 860 bonds, 105 residues, 1 model selected > delete atoms sel > delete bonds sel > select #9/C 83 atoms, 85 bonds, 9 residues, 1 model selected > delete atoms sel > delete bonds sel > select #9/D 1600 atoms, 1630 bonds, 212 residues, 1 model selected > delete atoms sel > delete bonds sel > select #9/E 1984 atoms, 2006 bonds, 278 residues, 1 model selected > delete atoms sel > delete bonds sel > select #9/A 2291 atoms, 2336 bonds, 295 residues, 1 model selected > delete atoms sel > delete bonds sel > matchmaker #6 to #9 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 6vmx, chain F (#9) with mhc, chain M (#6), sequence alignment score = 953.9 RMSD between 181 pruned atom pairs is 0.492 angstroms; (across all 182 pairs: 0.514) > show #8 models > hide #8 models > show #8 models > hide #8 models > show #6 models > hide #6 models > show #6 models > hide #6 models > show #6 models > hide #6 models > matchmaker #1-3,5-8#!4 to #9 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 6vmx, chain F (#9) with MASLSRPSLP (MOG1_10), chain M (#1), sequence alignment score = 957.5 RMSD between 182 pruned atom pairs is 0.498 angstroms; (across all 182 pairs: 0.498) Matchmaker 6vmx, chain F (#9) with LSRPSLPSCL (MOG4_13), chain M (#2), sequence alignment score = 957.5 RMSD between 182 pruned atom pairs is 0.542 angstroms; (across all 182 pairs: 0.542) Matchmaker 6vmx, chain F (#9) with KVTLRIRNVR (MOG109_118), chain M (#3), sequence alignment score = 957.5 RMSD between 181 pruned atom pairs is 0.477 angstroms; (across all 182 pairs: 0.533) Matchmaker 6vmx, chain F (#9) with APHTPLPPVS (1-B09), chain M (#5), sequence alignment score = 957.5 RMSD between 181 pruned atom pairs is 0.521 angstroms; (across all 182 pairs: 0.548) Matchmaker 6vmx, chain F (#9) with mhc, chain M (#6), sequence alignment score = 953.9 RMSD between 181 pruned atom pairs is 0.492 angstroms; (across all 182 pairs: 0.514) Matchmaker 6vmx, chain F (#9) with KPTPPPSRR (1-A08), chain M (#7), sequence alignment score = 957.5 RMSD between 181 pruned atom pairs is 0.526 angstroms; (across all 182 pairs: 0.546) Matchmaker 6vmx, chain F (#9) with TPTPPPQVP (A-A10), chain M (#8), sequence alignment score = 957.5 RMSD between 181 pruned atom pairs is 0.508 angstroms; (across all 182 pairs: 0.530) Matchmaker 6vmx, chain F (#9) with RPPIFIRRLH (1-A09), chain M (#4), sequence alignment score = 957.5 RMSD between 182 pruned atom pairs is 0.485 angstroms; (across all 182 pairs: 0.485) > show #5 models > hide #5 models > show #5 models > hide #5 models > show #6 models > hide #6 models > show #6 models > hide #6 models > select #9/H 83 atoms, 85 bonds, 9 residues, 1 model selected > show sel atoms > hide sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain #9/I Alignment identifier is 9/I > sequence chain #9/J Alignment identifier is 9/J > select #9/J:25 9 atoms, 8 bonds, 1 residue, 1 model selected > select #9/J:25-39 65 atoms, 66 bonds, 8 residues, 1 model selected > select #9/J:64-65 17 atoms, 16 bonds, 2 residues, 1 model selected > select #9/J:64-68 39 atoms, 38 bonds, 5 residues, 1 model selected > select #9/J:69 9 atoms, 8 bonds, 1 residue, 1 model selected > select #9/J:69-75 46 atoms, 46 bonds, 6 residues, 1 model selected > select #9/J:80 6 atoms, 5 bonds, 1 residue, 1 model selected > select #9/J:80-85 33 atoms, 33 bonds, 5 residues, 1 model selected > select #9/J:92-93 15 atoms, 15 bonds, 2 residues, 1 model selected > select #9/J:92-94 23 atoms, 23 bonds, 3 residues, 1 model selected > select #9/J:105 5 atoms, 4 bonds, 1 residue, 1 model selected > select #9/J:105-115 80 atoms, 81 bonds, 11 residues, 1 model selected > select #9/J:108 9 atoms, 8 bonds, 1 residue, 1 model selected > select #9/J:108-111 36 atoms, 36 bonds, 4 residues, 1 model selected > select #9/J:46 5 atoms, 4 bonds, 1 residue, 1 model selected > select #9/J:46-48 23 atoms, 22 bonds, 3 residues, 1 model selected > select #9/J:108-109 17 atoms, 16 bonds, 2 residues, 1 model selected > select #9/J:108-115 63 atoms, 64 bonds, 8 residues, 1 model selected > show sel atoms > style sel stick Changed 63 atom styles > style sel ball Changed 63 atom styles > style sel stick Changed 63 atom styles > color sel byhetero > select #9/J:69-70 15 atoms, 14 bonds, 2 residues, 1 model selected > select #9/J:69-75 46 atoms, 46 bonds, 6 residues, 1 model selected > select #9/J:45-46 14 atoms, 13 bonds, 2 residues, 1 model selected > select #9/J:45-50 46 atoms, 47 bonds, 6 residues, 1 model selected > select #9/J:25-26 19 atoms, 19 bonds, 2 residues, 1 model selected > select #9/J:25-37 52 atoms, 53 bonds, 6 residues, 1 model selected > select #9/J:15 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/J:15-18 32 atoms, 31 bonds, 4 residues, 1 model selected > select #9/J:69 9 atoms, 8 bonds, 1 residue, 1 model selected > select #9/J:69-75 46 atoms, 46 bonds, 6 residues, 1 model selected > select #9/J:80 6 atoms, 5 bonds, 1 residue, 1 model selected > select #9/J:80-85 33 atoms, 33 bonds, 5 residues, 1 model selected > select #9/I:45 9 atoms, 8 bonds, 1 residue, 1 model selected > select #9/I:45-50 43 atoms, 43 bonds, 6 residues, 1 model selected > select #9/I:57 7 atoms, 6 bonds, 1 residue, 1 model selected > select #9/I:57-64 35 atoms, 34 bonds, 5 residues, 1 model selected > select #9/I:68-74 13 atoms, 12 bonds, 2 residues, 1 model selected > select #9/I:68-75 24 atoms, 23 bonds, 3 residues, 1 model selected > select #9/I:82-83 16 atoms, 15 bonds, 2 residues, 1 model selected > select #9/I:82-85 29 atoms, 28 bonds, 4 residues, 1 model selected > select #9/I:15 9 atoms, 8 bonds, 1 residue, 1 model selected > select #9/I:15-18 27 atoms, 26 bonds, 4 residues, 1 model selected > select #9/I:25-26 18 atoms, 19 bonds, 2 residues, 1 model selected > select #9/I:25-29 38 atoms, 39 bonds, 5 residues, 1 model selected > select #9/I:141-142 15 atoms, 14 bonds, 2 residues, 1 model selected > select #9/I:141-146 44 atoms, 43 bonds, 6 residues, 1 model selected > select #9/I:109-110 14 atoms, 13 bonds, 2 residues, 1 model selected > select #9/I:109-113 34 atoms, 33 bonds, 5 residues, 1 model selected > select #9/I:83-84 18 atoms, 17 bonds, 2 residues, 1 model selected > select #9/I:83-85 22 atoms, 21 bonds, 3 residues, 1 model selected > select #9/I:109 6 atoms, 5 bonds, 1 residue, 1 model selected > select #9/I:109-113 34 atoms, 33 bonds, 5 residues, 1 model selected > style sel stick Changed 34 atom styles > show sel atoms > hide sel cartoons > show sel cartoons > color sel byhetero > select #9/F 2214 atoms, 2255 bonds, 1 pseudobond, 287 residues, 2 models selected > ui tool show ""Color Actions"" > color sel dark salmon > color sel light slate gray > color sel slate gray > ui tool show ""Color Actions"" > color (#!9 & sel) #fffffffe > color (#!9 & sel) #ffffffd5 > color (#!9 & sel) #ffffffcc > color (#!9 & sel) #ffffffb8 > color (#!9 & sel) #ffffff9f > color (#!9 & sel) #ffffff8e > color (#!9 & sel) #ffffff88 > color (#!9 & sel) #ffffff87 > color (#!9 & sel) #ffffff85 > color (#!9 & sel) #ffffff83 > color (#!9 & sel) #ffffff82 > color (#!9 & sel) #ffffff81 > color (#!9 & sel) #ffffff80 > color (#!9 & sel) #ffffff88 > color (#!9 & sel) #ffffff8c > color (#!9 & sel) #ffffff8f > color (#!9 & sel) #ffffff91 > color (#!9 & sel) #ffffff93 > color (#!9 & sel) #ffffff96 > color (#!9 & sel) #ffffff98 > color (#!9 & sel) #ffffff9c > color (#!9 & sel) #ffffffa4 > color (#!9 & sel) #ffffffa9 > color (#!9 & sel) #ffffffab > color (#!9 & sel) #ffffffac > color (#!9 & sel) #ffffffad > color (#!9 & sel) #ffffffaf > color (#!9 & sel) #ffffffb1 > color (#!9 & sel) #ffffffb5 > color (#!9 & sel) #ffffffb6 > color (#!9 & sel) #ffffffb7 > color (#!9 & sel) #ffffffba > color (#!9 & sel) #ffffffbb > color (#!9 & sel) #ffffffb9 > color (#!9 & sel) #ffffffb8 > color (#!9 & sel) #ffffffb6 > color (#!9 & sel) #ffffffb1 > color (#!9 & sel) #ffffffae > color (#!9 & sel) #ffffffab > color (#!9 & sel) #ffffffaa > color (#!9 & sel) #ffffffa8 > color (#!9 & sel) #ffffffa6 > color (#!9 & sel) #ffffffa4 > color (#!9 & sel) #ffffffa3 > color (#!9 & sel) #ffffffa2 > color (#!9 & sel) #ffffffa1 > color (#!9 & sel) #ffffffa0 > color (#!9 & sel) #ffffff9e > color (#!9 & sel) #ffffff9d > color (#!9 & sel) #ffffff9c > color (#!9 & sel) #ffffff9b > color (#!9 & sel) #ffffff99 > color (#!9 & sel) #ffffff98 > color (#!9 & sel) #ffffff97 > color (#!9 & sel) #ffffff98 > color (#!9 & sel) #ffffff99 > color (#!9 & sel) #ffffff9a > color (#!9 & sel) #ffffff9c > color (#!9 & sel) #ffffff9d > color (#!9 & sel) #ffffff9e > color (#!9 & sel) #ffffff9f > color (#!9 & sel) #ffffffa1 > color (#!9 & sel) #ffffffa6 > color (#!9 & sel) #ffffffa8 > color (#!9 & sel) #ffffffa9 > color (#!9 & sel) #ffffffaa > color (#!9 & sel) #ffffffac > color (#!9 & sel) #ffffffae > color (#!9 & sel) #ffffffaf > color (#!9 & sel) #ffffffb0 > color (#!9 & sel) #ffffffb2 > color (#!9 & sel) #ffffffb3 > color (#!9 & sel) #ffffffb2 > color (#!9 & sel) #a9a9a9ff > color (#!9 & sel) #76d6ffff > color (#!9 & sel) #76d6ffde > color (#!9 & sel) #76d6ffbc > color (#!9 & sel) #76d6ffa3 > color (#!9 & sel) #76d6ff99 > color (#!9 & sel) #76d6ff8e > color (#!9 & sel) #76d6ff81 > color (#!9 & sel) #76d6ff77 > color (#!9 & sel) #76d6ff72 > color (#!9 & sel) #76d6ff70 > color (#!9 & sel) #76d6ff6f > color (#!9 & sel) #76d6ff6e > color (#!9 & sel) #76d6ff6b > color (#!9 & sel) #76d6ff60 > color (#!9 & sel) #76d6ff55 > color (#!9 & sel) #76d6ff4f > color (#!9 & sel) #76d6ff4e > color (#!9 & sel) #76d6ff4d > color (#!9 & sel) #76d6ff4c > color (#!9 & sel) #76d6ff4b > color (#!9 & sel) #76d6ff4a > color (#!9 & sel) #76d6ff49 > color (#!9 & sel) #76d6ff48 > color (#!9 & sel) #76d6ff47 > color (#!9 & sel) #76d6ff46 > color (#!9 & sel) #76d6ff45 > color (#!9 & sel) #76d6ff46 > color (#!9 & sel) #76d6ff47 > color (#!9 & sel) #76d6ff48 > color (#!9 & sel) #76d6ff49 > color (#!9 & sel) #76d6ff4b > color (#!9 & sel) #76d6ff4c > color (#!9 & sel) #76d6ff4e > color (#!9 & sel) #76d6ff4f > color (#!9 & sel) #76d6ff50 > color (#!9 & sel) #76d6ff51 > color (#!9 & sel) #76d6ff53 > color (#!9 & sel) #76d6ff54 > color (#!9 & sel) #76d6ff56 > color (#!9 & sel) #76d6ff58 > color (#!9 & sel) #76d6ff59 > color (#!9 & sel) #76d6ff5b > color (#!9 & sel) #76d6ff5c > color (#!9 & sel) #76d6ff5e > color (#!9 & sel) #76d6ff5f > color (#!9 & sel) #76d6ff61 > color (#!9 & sel) #76d6ff62 > color (#!9 & sel) #76d6ff63 > color (#!9 & sel) #76d6ff5e > color (#!9 & sel) #76d6ff5b > color (#!9 & sel) #76d6ff58 > color (#!9 & sel) #76d6ff55 > color (#!9 & sel) #76d6ff52 > color (#!9 & sel) #76d6ff4d > color (#!9 & sel) #76d6ff43 > color (#!9 & sel) #76d6ff3e > color (#!9 & sel) #76d6ff3c > color (#!9 & sel) #76d6ff3b > color (#!9 & sel) #76d6ff39 > color (#!9 & sel) #76d6ff35 > color (#!9 & sel) #76d6ff31 > color (#!9 & sel) #76d6ff2f > color (#!9 & sel) #76d6ff2e > color (#!9 & sel) #76d6ff2f > color (#!9 & sel) #76d6ff33 > color (#!9 & sel) #76d6ff34 > color (#!9 & sel) #76d6ff36 > color (#!9 & sel) #76d6ff39 > color (#!9 & sel) #76d6ff3d > color (#!9 & sel) #76d6ff40 > color (#!9 & sel) #76d6ff3f > color (#!9 & sel) #76d6ff3e > color (#!9 & sel) #76d6ff3c > color (#!9 & sel) #76d6ff3b > color (#!9 & sel) #76d6ff3c > color (#!9 & sel) #76d6ff3d > color (#!9 & sel) #76d6ff46 > color (#!9 & sel) #76d6ff51 > color (#!9 & sel) #76d6ff58 > color (#!9 & sel) #76d6ff5a > color (#!9 & sel) #76d6ff5b > color (#!9 & sel) #76d6ff5f > color (#!9 & sel) #76d6ff63 > color (#!9 & sel) #76d6ff64 > color (#!9 & sel) #76d6ff66 > color (#!9 & sel) #76d6ff68 > color (#!9 & sel) #76d6ff6a > color (#!9 & sel) #76d6ff6b > color (#!9 & sel) #76d6ff68 > color (#!9 & sel) #76d6ff67 > color (#!9 & sel) #76d6ff66 > color (#!9 & sel) #76d6ff64 > color (#!9 & sel) #76d6ff63 > color (#!9 & sel) #76d6ff61 > color (#!9 & sel) #76d6ff60 > color (#!9 & sel) #76d6ff5f > color (#!9 & sel) #76d6ff5d > color (#!9 & sel) #76d6ff60 > color (#!9 & sel) #76d6ff62 > color (#!9 & sel) #76d6ff6c > color (#!9 & sel) #76d6ff7a > color (#!9 & sel) #76d6ff84 > color (#!9 & sel) #76d6ff86 > color (#!9 & sel) #76d6ff85 > color (#!9 & sel) #76d6ff84 > color (#!9 & sel) #76d6ff83 > color (#!9 & sel) #76d6ff82 > color (#!9 & sel) #76d6ff81 > color (#!9 & sel) #76d6ff80 > color (#!9 & sel) #76d6ff76 > color (#!9 & sel) #76d6ff72 > color (#!9 & sel) #76d6ff6d > color (#!9 & sel) #76d6ff66 > color (#!9 & sel) #76d6ff61 > color (#!9 & sel) #76d6ff5f > color (#!9 & sel) #76d6ff5e > color (#!9 & sel) #76d6ff59 > color (#!9 & sel) #76d6ff51 > color (#!9 & sel) #76d6ff4a > color (#!9 & sel) #76d6ff48 > color (#!9 & sel) #76d6ff47 > color sel sea green > color sel medium sea green > color sel sea green > select #9/I 1608 atoms, 1630 bonds, 220 residues, 1 model selected > color sel chocolate > color sel sienna > color sel byhetero > select #9/J 1964 atoms, 1998 bonds, 265 residues, 1 model selected > color sel coral > color sel tomato > color sel salmon > color sel dodger blue > color sel turquoise > color sel medium turquoise > color sel orange > color sel dark orange > color sel goldenrod > color sel sandy brown > color sel byhetero > select #9/H 83 atoms, 85 bonds, 9 residues, 1 model selected > color sel spring green > color sel blue > color sel medium blue > color sel slate gray > color sel dark blue > color sel medium blue > color sel dark blue > color sel navy > color sel indigo > color sel royal blue > color sel deep sky blue > color sel royal blue > color sel slate blue > color sel dark violet > color sel deep pink > color sel dark slate blue > color sel slate blue > color sel dark slate blue > color sel slate blue > color sel medium slate blue > color sel dark slate gray > color sel aquamarine > color sel sky blue > color sel light sky blue > color sel honeydew > color sel alice blue > color sel light pink > color sel lavender > color sel rebecca purple > color sel dark slate blue > color sel rebecca purple > color sel midnight blue > color sel royal blue > color sel byhetero > color sel medium orchid > color sel orchid > color sel pale violet red > color sel byhetero > select clear > movie record > turn y 2 180 > wait 180 > movie encode /Users/philippnawrath/Desktop/movie1.mp4 Movie saved to /Users/philippnawrath/Desktop/movie1.mp4 > ui tool show ""Side View"" > view orient > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting full > lighting flat > lighting full > lighting flat > lighting full > lighting soft > lighting simple > lighting shadows true > lighting shadows false > lighting flat > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting flat > lighting full > lighting flat > lighting soft > lighting simple > lighting soft > lighting full > undo > set bgColor white > set bgColor black > set bgColor gray > set bgColor black > set bgColor white > select clear > lighting simple > lighting soft > lighting simple > lighting full > lighting flat > lighting full > graphics silhouettes false > lighting full > lighting soft > lighting simple > lighting soft > lighting full > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting full > lighting simple > lighting flat > lighting full > lighting soft > lighting simple > lighting flat > lighting simple > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting simple > select #9/H 83 atoms, 85 bonds, 9 residues, 1 model selected > center sel Unknown command: center sel > cofr Center of rotation: -71.854 -9.2962 5.222 front center > select clear > movie record > turn y 2 180 > wait 180 > movie encode /Users/philippnawrath/Desktop/movie2.mp4 Movie saved to /Users/philippnawrath/Desktop/movie2.mp4 > show #5 models > hide #!9 models > show #6 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #6 models > show #!9 models > hide #5 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!9 models > hide #!4 models > show #3 models > hide #3 models > show #6 models > show #3 models > hide #3 models > show #3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields still retrieving bundle list from toolshed > isolde shorthand Error running startup command 'isolde shorthand': Unknown command: isolde shorthand 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 - 89.3 OpenGL renderer: Apple M2 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: Mac14,2 Model Number: Z15S000LJSM/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.1 (24D70) Kernel Version: Darwin 24.3.0 Time since boot: 77 days, 6 hours, 25 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2423DE: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported 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