id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9198 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.3-arm64-arm-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000002b2ed3000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000002b1ec7000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000002b0ebb000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000002afeaf000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000002aeea3000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000002ade97000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000002ace8b000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000002abe7f000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000002aae73000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000002a9e67000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000002a8e5b000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000002a7e4f000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000029c8cb000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x0000000104cc0580 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", 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""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000005 } ] } } ===== 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 UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Updating list of available bundles failed: Internal Server Error > open 7WCO Summary of feedback from opening 7WCO fetched from pdb --- note | Fetching compressed mmCIF 7wco from http://files.rcsb.org/download/7wco.cif 7wco title: Cryo-EM structure of alphavirus, Getah virus [more info...] Chain information for 7wco #1 --- Chain | Description | UniProt J | Spike glycoprotein E1 | POLS_GETV 1-438 K | Spike glycoprotein E2 | POLS_GETV 1-422 L | Capsid protein | POLS_GETV 1-268 7wco mmCIF Assemblies --- 1| complete point assembly 2| point asymmetric unit 3| point asymmetric unit, std point frame > close 7wco Expected a models specifier or a keyword > open 7FD2 Summary of feedback from opening 7FD2 fetched from pdb --- notes | Fetching compressed mmCIF 7fd2 from http://files.rcsb.org/download/7fd2.cif Fetching CCD NAG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif Fetching CCD BMA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif Fetching CCD MAN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif Fetching CCD PCW from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/PCW/PCW.cif Fetching CCD STE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/STE/STE.cif Fetching CCD PLM from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/PLM/PLM.cif Fetching CCD CLR from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/CLR/CLR.cif 7fd2 title: Cryo-EM structure of an alphavirus, Getah virus [more info...] Chain information for 7fd2 #2 --- Chain | Description | UniProt A E I M | Envelope glycoprotein 1 | A0A1Z2R994_GETV 1-438 B F J N | Envelope glycoprotein 2 | A0A1Z2R994_GETV 1-419 C G K O | capsid protein | A0A1Z2R994_GETV 1-268 Non-standard residues in 7fd2 #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CLR — cholesterol MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PCW — 1,2-dioleoyl-Sn-glycero-3-phosphocholine ((Z,Z)-4-hydroxy-N,N,N-trimethyl-10-oxo-7-[(1-oxo-9-octadecenyl)oxy]-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium-4-oxide) PLM — palmitic acid STE — stearic acid 7fd2 mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame > hide #1 models > hide #2 models > show #2 models > show #2 target m > select add #2 32613 atoms, 33504 bonds, 4136 residues, 1 model selected > select subtract #2 Nothing selected > sym #2 assembly 2 Made 1 copies for 7fd2 assembly 2 > view > show target m > rename #3 GETV_ASU > show sequence Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > sym #2 assembly 5 Made 1 copies for 7fd2 assembly 5 > view > hide #3.1 models > show #3.1 models > hide #3.1 models > ui tool show ""Selection Inspector"" > sequence chainn Missing or invalid ""chains"" argument: empty atom specifier > 7fd2 Unknown command: sequence 7fd2 > sequence chain #2/A#2/E#2/I#2/M Alignment identifier is 1 > select > #2/A,E,I,M:2-8,14-19,24-25,27-48,51-54,59-61,77-82,101-110,119-136,142-147,153-156,159-163,176-180,183-186,203-205,213-215,220-221,233-234,260-262,267-269,275-281,288-289,297-306,314-321,326-332,337-339,343-346,351-358,364-369,374-377,387-388 5596 atoms, 5584 bonds, 716 residues, 1 model selected > hide #!4 models > show #!4 models > view #4 clip false > hide #!3 models > hide #1 models > hide #!4 models > show #!4 models > hide #4.1 models > show #4.1 models > select #2/A,E,I,M:4-5 48 atoms, 44 bonds, 8 residues, 1 model selected > select #2/A,E,I,M:4-19 488 atoms, 504 bonds, 64 residues, 1 model selected > view #4 clip false > select > #2/A,E,I,M:2-8,14-19,24-25,27-48,51-54,59-61,77-82,101-110,119-136,142-147,153-156,159-163,176-180,183-186,203-205,213-215,220-221,233-234,260-262,267-269,275-281,288-289,297-306,314-321,326-332,337-339,343-346,351-358,364-369,374-377,387-388 5596 atoms, 5584 bonds, 716 residues, 1 model selected > style #4.1 stick Changed 32613 atom styles > style #4.1 stick Changed 32613 atom styles > style #4.1 sphere Changed 32613 atom styles > style #4.1 ball Changed 32613 atom styles > style #4.1 sphere Changed 32613 atom styles > show #4.1 cartoons > show #4.1 atoms > style #4.1 stick Changed 32613 atom styles > style #4.1 sphere Changed 32613 atom styles > close session > open 7FD2 format mmcif fromDatabase pdb 7fd2 title: Cryo-EM structure of an alphavirus, Getah virus [more info...] Chain information for 7fd2 #1 --- Chain | Description | UniProt A E I M | Envelope glycoprotein 1 | A0A1Z2R994_GETV 1-438 B F J N | Envelope glycoprotein 2 | A0A1Z2R994_GETV 1-419 C G K O | capsid protein | A0A1Z2R994_GETV 1-268 Non-standard residues in 7fd2 #1 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CLR — cholesterol MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PCW — 1,2-dioleoyl-Sn-glycero-3-phosphocholine ((Z,Z)-4-hydroxy-N,N,N-trimethyl-10-oxo-7-[(1-oxo-9-octadecenyl)oxy]-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium-4-oxide) PLM — palmitic acid STE — stearic acid 7fd2 mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame > select /A:1-438 3333 atoms, 3424 bonds, 438 residues, 1 model selected > select /A:1-438 3333 atoms, 3424 bonds, 438 residues, 1 model selected > select /A:1-438 3333 atoms, 3424 bonds, 438 residues, 1 model selected > sequence chain #1/A#1/E#1/I#1/M Alignment identifier is 1 > select /A:1-438 3333 atoms, 3424 bonds, 438 residues, 1 model selected > select Y1 Expected an objects specifier or a keyword > select /A,E,I,M:241-286 1400 atoms, 1432 bonds, 184 residues, 1 model selected > select /A,E,I,M:241-286 1400 atoms, 1432 bonds, 184 residues, 1 model selected > select > /A,E,I,M:2-8,14-19,24-25,27-48,51-54,59-61,77-82,101-110,119-136,142-147,153-156,159-163,176-180,183-186,203-205,213-215,220-221,233-234,260-262,267-269,275-281,288-289,297-306,314-321,326-332,337-339,343-346,351-358,364-369,374-377,387-388 5596 atoms, 5584 bonds, 716 residues, 1 model selected > select /A,E,I,M:241-286 1400 atoms, 1432 bonds, 184 residues, 1 model selected > select /A,E,I,M:152 40 atoms, 40 bonds, 4 residues, 1 model selected > select /A,E,I,M:152 40 atoms, 40 bonds, 4 residues, 1 model selected > select > /A,E,I,M:2-8,14-19,24-25,27-48,51-54,59-61,77-82,101-110,119-136,142-147,153-156,159-163,176-180,183-186,203-205,213-215,220-221,233-234,260-262,267-269,275-281,288-289,297-306,314-321,326-332,337-339,343-346,351-358,364-369,374-377,387-388 5596 atoms, 5584 bonds, 716 residues, 1 model selected > select /A,E,I,M:345-346 64 atoms, 60 bonds, 8 residues, 1 model selected > select /A,E,I,M:345-346 64 atoms, 60 bonds, 8 residues, 1 model selected > select /A,E,I,M:345-346 64 atoms, 60 bonds, 8 residues, 1 model selected > select /A,E,I,M:345-346 64 atoms, 60 bonds, 8 residues, 1 model selected > select /A,E,I,M:345-346 64 atoms, 60 bonds, 8 residues, 1 model selected > select /A,E,I,M:345-346 64 atoms, 60 bonds, 8 residues, 1 model selected > show sel atoms > select /A,E,I,M:348 28 atoms, 24 bonds, 4 residues, 1 model selected > select /A,E,I,M:345-348 128 atoms, 124 bonds, 16 residues, 1 model selected > show sel atoms > select /A,E,I,M:345 32 atoms, 28 bonds, 4 residues, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > select all 32613 atoms, 33504 bonds, 4136 residues, 1 model selected > hide sel atoms > show sel atoms > hide sel cartoons > style sel stick Changed 32613 atom styles > select /A,E,I,M:345 32 atoms, 28 bonds, 4 residues, 1 model selected > select /A,E,I,M:347 36 atoms, 32 bonds, 4 residues, 1 model selected > select /A,E,I,M:345 32 atoms, 28 bonds, 4 residues, 1 model selected > addcharge charge /A,E,I,M:345 Expected a keyword > zoom 2 > style sel sphere Changed 32 atom styles > style sel stick Changed 32 atom styles > style sel ball Changed 32 atom styles > color sel byhetero > select/ A:325 Unknown command: select/ A:325 > select /A:325 7 atoms, 7 bonds, 1 residue, 1 model selected > select /A:327 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > open 8IHP Summary of feedback from opening 8IHP fetched from pdb --- notes | Fetching compressed mmCIF 8ihp from http://files.rcsb.org/download/8ihp.cif Fetching CCD CA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif 8ihp title: Structure of Semliki Forest virus VLP in complex with the receptor VLDLR-LA3 [more info...] Chain information for 8ihp #2 --- Chain | Description | UniProt A D G J | Spike glycoprotein E2 | POLS_SFV 1-422 B E H K | Spike glycoprotein E1 | POLS_SFV 1-438 C F I L | Capsid protein | POLS_SFV 106-267 M N O | Very low-density lipoprotein receptor | VLDLR_HUMAN 111-149 Non-standard residues in 8ihp #2 --- CA — calcium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > zoom 0.5 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > ui mousemode right zoom > ui tool show Matchmaker > matchmaker #1 to #2 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 8ihp, chain H (#2) with 7fd2, chain I (#1), sequence alignment score = 1863 RMSD between 425 pruned atom pairs is 0.764 angstroms; (across all 437 pairs: 0.874) > matchmaker #1 to #2 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 8ihp, chain H (#2) with 7fd2, chain I (#1), sequence alignment score = 1863 RMSD between 425 pruned atom pairs is 0.764 angstroms; (across all 437 pairs: 0.874) > ui mousemode right translate > ui mousemode right rotate > ui mousemode right zoom > ui mousemode right translate > hide 2/M Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #2/M > hide #2/M, N, O > style sel stick Changed 9 atom styles > show #2 sticks Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #2/ sticks > style #2 sticks Expected a keyword > style #2 stick Changed 32337 atom styles > ui mousemode right zoom > select #1/A:345 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:345 4 atoms, 3 bonds, 1 residue, 1 model selected > hide #2/A,D,G,J > hide #2/C,F,I,L > hide #1/B,F,J,N > ui mousemode right select > color #2 purple > color #2 magenta > color #1 orange > ui mousemode right zoom > ui mousemode right translate > hide #2 > show #2/E > hide #1 > show #1/E > show #1/A > show #1/E > hide #1/E > color sel byhetero > select #1/A: 345, 347, 327 26 atoms, 23 bonds, 3 residues, 1 model selected > color sel byhetero > backbone only #1 Unknown command: backbone only #1 > show only backbone #1 Expected a keyword > hide side chain #1 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide side chain #1/E Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide side chain #1/A Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > hide sel atoms > show sel atoms > hide sel atoms > show sel atoms > hide sel atoms > show sel atoms > ui mousemode right zoom > ui mousemode right select > ui mousemode right zoom Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Updating list of available bundles failed: Internal Server Error OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 7459.101.2 OS Loader Version: 7459.101.2 Software: System Software Overview: System Version: macOS 12.3 (21E230) Kernel Version: Darwin 21.4.0 Time since boot: 14 days 11 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: S34J55x: Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD) UI Looks like: 3440 x 1440 @ 50.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 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: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX