id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14592 Crash in garbage collection x.aran-guiu@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.3.1-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff84507c7c0 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in __iter__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 907 in atomspec_atoms File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 627 in _add_model_parts File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 476 in _check File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 490 in _check File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 470 in find_matches File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 612 in find_matches File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 455 in find_matches File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1004 in find_matches File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1001 in evaluate File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1091 in evaluate File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py"", line 36 in parse File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py"", line 71 in parse File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2499 in _parse_arg File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2640 in _process_positional_arguments File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2864 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py"", line 303 in run_matchmaker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 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, chimerax.geometry._geometry, 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Bytes before following region: 140737486995287\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffeb4000-7fffffeb5000 [ 4K] r-x\/r-x SM=SHM "", ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a9"",""rawCodes"":[1,169],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a9""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":57851}, ""ktriageinfo"" : ""VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n"", ""vmregioninfo"" : ""0xa9 is not in any region. 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""f14a449c0eca842325edf82f799b756ac67e0279"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""632e3f9c01482c74ed76392d"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""65b9907b1f4f6a3a095cb4d5"" }, ""deploymentId"" : 240000390 }, { ""rolloutId"" : ""63508950b3714d3622fc77f7"", ""factorPackIds"" : { ""SIRI_MEMORY_SYNC_CONFIG"" : ""6526e111d0c9ce2f459b54a8"" }, ""deploymentId"" : 240000014 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > device snav true > open pdb:5lho Summary of feedback from opening 5lho fetched from pdb --- warning | PDB entry 5LHO has been replaced by 5LVZ note | Fetching compressed mmCIF 5lho from http://files.rcsb.org/download/5lho.cif 5lho title: Crystal structure of yeast 14-3-3 protein (Bmh1) from Lachancea thermotolerans [more info...] Chain information for 5lho #1 --- Chain | Description | UniProt A | KLTH0G14146p | C5DN49_LACTC 1-253 5lho mmCIF Assemblies --- 1| author_and_software_defined_assembly > close > open pdb:5loh Summary of feedback from opening 5loh fetched from pdb --- notes | Fetching compressed mmCIF 5loh from http://files.rcsb.org/download/5loh.cif Fetching CCD CL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif 5loh title: Kinase domain of human Greatwall [more info...] Chain information for 5loh #1 --- Chain | Description | UniProt A B | Serine/threonine-protein kinase greatwall,Serine/threonine-protein kinase greatwall | GWL_HUMAN 1-735 740-879 Non-standard residues in 5loh #1 --- CL — chloride ion EDO — 1,2-ethanediol (ethylene glycol) STU — staurosporine 5loh mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > set bgColor white > lighting flat > lighting full > select #1/A 1949 atoms, 1972 bonds, 3 pseudobonds, 282 residues, 2 models selected > select #1/b 1988 atoms, 2019 bonds, 2 pseudobonds, 278 residues, 2 models selected > hide cartoons > hide sel cartoons > hide sel > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B Alignment identifier is 1 > select clear > open alphafold:Q96GX5-F1 UniProt identifiers must be 6 or 10 characters long, got ""Q96GX5-F1"" > open alphafold:Q96GX5 Summary of feedback from opening Q96GX5 fetched from alphafold --- note | Fetching compressed AlphaFold Q96GX5 from https://alphafold.ebi.ac.uk/files/AF-Q96GX5-F1-model_v4.cif Chain information for AlphaFold Q96GX5 #2 --- Chain | Description | UniProt A | Serine/threonine-protein kinase greatwall | GWL_HUMAN 1-879 Color AlphaFold Q96GX5 by residue attribute pLDDT_score > ui tool show Matchmaker > matchmaker #2 to #1 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 5loh, chain B (#1) with AlphaFold Q96GX5, chain A (#2), sequence alignment score = 967.6 RMSD between 227 pruned atom pairs is 0.671 angstroms; (across all 250 pairs: 1.591) > hide #!1 models > show #!1 models > hide #!1 models > hide #2 models > show #2 models > show #!1 models > 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 AlphaFold Q96GX5, chain A (#2) with 5loh, chain B (#1), sequence alignment score = 967.6 RMSD between 227 pruned atom pairs is 0.671 angstroms; (across all 250 pairs: 1.591) > 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 AlphaFold Q96GX5, chain A (#2) with 5loh, chain B (#1), sequence alignment score = 967.6 RMSD between 227 pruned atom pairs is 0.671 angstroms; (across all 250 pairs: 1.591) > 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 AlphaFold Q96GX5, chain A (#2) with 5loh, chain B (#1), sequence alignment score = 967.6 RMSD between 227 pruned atom pairs is 0.671 angstroms; (across all 250 pairs: 1.591) > matchmaker #2/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 5loh, chain A (#1) with AlphaFold Q96GX5, chain A (#2), sequence alignment score = 964 RMSD between 225 pruned atom pairs is 0.718 angstroms; (across all 248 pairs: 4.860) > hide #!1 models > show #!1 models > save ""/Users/xavieraranguiu/Dropbox > (Strubiol)/XA_Experiments/EXA176_240209_Cloning new kinases > set/MASTL_structures.cxs"" > close > open alphafold:O75460 Summary of feedback from opening O75460 fetched from alphafold --- note | Fetching compressed AlphaFold O75460 from https://alphafold.ebi.ac.uk/files/AF-O75460-F1-model_v4.cif Chain information for AlphaFold O75460 #1 --- Chain | Description | UniProt A | Serine/threonine-protein kinase/endoribonuclease IRE1 | ERN1_HUMAN 1-977 Color AlphaFold O75460 by residue attribute pLDDT_score > close > open alphafold:O75460 Chain information for AlphaFold O75460 #1 --- Chain | Description | UniProt A | Serine/threonine-protein kinase/endoribonuclease IRE1 | ERN1_HUMAN 1-977 Color AlphaFold O75460 by residue attribute pLDDT_score > open pdb:2hz6,3p23, 6w39 PDB identifiers are either 4 or 8 characters long, got ""2hz6,3p23,"" > open pdb:2hz6, 3p23, 6w39 '3p23,' has no suffix > open pdb:2hz6 Summary of feedback from opening 2hz6 fetched from pdb --- note | Fetching compressed mmCIF 2hz6 from http://files.rcsb.org/download/2hz6.cif 2hz6 title: The crystal structure of human IRE1-alpha luminal domain [more info...] Chain information for 2hz6 #2 --- Chain | Description | UniProt A | Endoplasmic reticulum to nucleus signalling 1 isoform 1 variant | Q59EE2_HUMAN 24-390 2hz6 mmCIF Assemblies --- 1| author_defined_assembly > open pdb:3p23 Summary of feedback from opening 3p23 fetched from pdb --- notes | Fetching compressed mmCIF 3p23 from http://files.rcsb.org/download/3p23.cif Fetching CCD ADP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ADP/ADP.cif 3p23 title: Crystal structure of the Human kinase and RNase domains in complex with ADP [more info...] Chain information for 3p23 #3 --- Chain | Description | UniProt A B C D | Serine/threonine-protein kinase/endoribonuclease IRE1 | ERN1_HUMAN 547-964 547-965 547-977 Non-standard residues in 3p23 #3 --- ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion 3p23 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| software_defined_assembly 4| software_defined_assembly 5| software_defined_assembly 6| software_defined_assembly > open pdb:6w39 Summary of feedback from opening 6w39 fetched from pdb --- note | Fetching compressed mmCIF 6w39 from http://files.rcsb.org/download/6w39.cif 6w39 title: Structure of unphosphorylated IRE1 in complex with G-1749 [more info...] Chain information for 6w39 #4 --- Chain | Description | UniProt A B | Serine/threonine-protein kinase/endoribonuclease IRE1 | ERN1_HUMAN 547-977 Non-standard residues in 6w39 #4 --- SJG — ethyl ~{N}-[6-methyl-5-[3-[2-[[(3~{S})-piperidin-3-yl]amino]pyrimidin-4-yl]pyridin-2-yl]oxy- naphthalen-1-yl]carbamate > matchmaker #2/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 AlphaFold O75460, chain A (#1) with 2hz6, chain A (#2), sequence alignment score = 1534.3 RMSD between 218 pruned atom pairs is 0.823 angstroms; (across all 253 pairs: 3.116) > matchmaker #3/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 AlphaFold O75460, chain A (#1) with 3p23, chain A (#3), sequence alignment score = 2035.1 RMSD between 277 pruned atom pairs is 0.935 angstroms; (across all 386 pairs: 2.846) > matchmaker #4/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 AlphaFold O75460, chain A (#1) with 6w39, chain A (#4), sequence alignment score = 2091.3 RMSD between 364 pruned atom pairs is 0.805 angstroms; (across all 374 pairs: 1.134) > hide #!3 models > hide #!4 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > show #!4 models > hide #!4 models > show #1 models > hide #1 models > select #3/B-D 9682 atoms, 9613 bonds, 15 pseudobonds, 1466 residues, 3 models selected > hide sel > cartoon hide (#!3 & sel) > hide #!3 models > show #!4 models > select #4/B-C 6040 atoms, 5914 bonds, 4 pseudobonds, 575 residues, 2 models selected > select #4/B-D 6040 atoms, 5914 bonds, 4 pseudobonds, 575 residues, 2 models selected > select #4/B 6040 atoms, 5914 bonds, 4 pseudobonds, 575 residues, 2 models selected > hide sel > hide sel cartoons > show #1 models > show #!2 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!4 models > show #!3 models > hide #!2 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 > open 5loh 5loh title: Kinase domain of human Greatwall [more info...] Chain information for 5loh #5 --- Chain | Description | UniProt A B | Serine/threonine-protein kinase greatwall,Serine/threonine-protein kinase greatwall | GWL_HUMAN 1-735 740-879 Non-standard residues in 5loh #5 --- CL — chloride ion EDO — 1,2-ethanediol (ethylene glycol) STU — staurosporine 5loh mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > matchmaker #5/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 AlphaFold O75460, chain A (#1) with 5loh, chain A (#5), sequence alignment score = 240.7 RMSD between 134 pruned atom pairs is 1.034 angstroms; (across all 233 pairs: 12.016) > hide #5/B > hide cartoons #5/B Expected ',' or a keyword > select #5/B 1988 atoms, 2019 bonds, 2 pseudobonds, 278 residues, 2 models selected > hide cartoon|sel Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide cartoons | sel Expected ',' or a keyword > hide cartoons > cartoon hide (#!5 & sel) > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!4 models > hide #!3 models > show #!5 models > hide #!5 models > hide #!4 models > show #1 models > close #5 > show #!2 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #!2 models > show #!2 models > show #!3 models > show #!4 models > hide #1 models > hide #!4 models > save ""/Users/xavieraranguiu/Dropbox > (Strubiol)/XA_Experiments/EXA176_240209_Cloning new kinases > set/IRE1a_structures.cxs"" > close > device snav false > open alphafold:Q9BQI3 Summary of feedback from opening Q9BQI3 fetched from alphafold --- note | Fetching compressed AlphaFold Q9BQI3 from https://alphafold.ebi.ac.uk/files/AF-Q9BQI3-F1-model_v4.cif Chain information for AlphaFold Q9BQI3 #1 --- Chain | Description | UniProt A | Eukaryotic translation initiation factor 2-alpha kinase 1 | E2AK1_HUMAN 1-630 Color AlphaFold Q9BQI3 by residue attribute pLDDT_score > open 5loh 5loh title: Kinase domain of human Greatwall [more info...] Chain information for 5loh #2 --- Chain | Description | UniProt A B | Serine/threonine-protein kinase greatwall,Serine/threonine-protein kinase greatwall | GWL_HUMAN 1-735 740-879 Non-standard residues in 5loh #2 --- CL — chloride ion EDO — 1,2-ethanediol (ethylene glycol) STU — staurosporine 5loh mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > ui tool show Matchmaker ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-5.2.5 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2020.80.5.0.1 (iBridge: 21.16.3049.0.0,0) OS Loader Version: 580~1337 Software: System Software Overview: System Version: macOS 14.3.1 (23D60) Kernel Version: Darwin 23.3.0 Time since boot: 3 hours, 11 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: DELL U3417W: Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD) UI Looks like: 3440 x 1440 @ 50.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 660X88B204LL Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 7.55 Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 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: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 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: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 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: 1.1.3 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: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 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: 2.2.2 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: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 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: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 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: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core fixed Tom Goddard all ChimeraX