id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14806 Crash in garbage collection tomyuhao@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.0-x86_64-i386-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 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 0x00007ff85dcf4e80 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py"", line 81 in msgpack_deserialize File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 721 in restore File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 1017 in open File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 37 in open File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 484 in remember_data_format File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 514 in collated_open File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 213 in provider_open File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 131 in cmd_open File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py"", line 464 in cxcmd File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py"", line 446 in defer File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 375 in thread_safe File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py"", line 455 in chimerax_intercept File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py"", line 353 in intercept File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py"", line 93 in _intercept File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py"", line 320 in interceptRequest File ""/Applications/ChimeraX-1.7.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.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.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, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, 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Bytes before following region: 140737487458135\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff25000-7ffffff26000 [ 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"":41589}, ""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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""63508beab3714d3622fc7808"" }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/laotangmu233/Desktop/labelled RABV-G stracture at normal > pH.pdb"" format pdb labelled RABV-G stracture at normal pH.pdb title: Structure of rabies virus glycoprotein At basic pH [more info...] Chain information for labelled RABV-G stracture at normal pH.pdb #1 --- Chain | Description | UniProt A B | glycoprotein,glycoprotein,glycoprotein | Q5JZZ2_9RHAB 1-74, Q2Z2I1_9RHAB 80-120, D8VEC1_9RHAB 126-439 > close > open 6LGW format mmcif fromDatabase pdb 6lgw title: Structure of Rabies virus glycoprotein in complex with neutralizing antibody 523-11 at acidic pH [more info...] Chain information for 6lgw #1 --- Chain | Description | UniProt A C | scFv 523-11 | E F | Glycoprotein | Q5JZZ2_9RHAB 1-74, Q2Z2I1_9RHAB 80-120, D8VEC1_9RHAB 126-405 6lgw mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > select /A:1-224 1720 atoms, 1763 bonds, 1 pseudobond, 222 residues, 2 models selected > hide sel cartoons > select /C:1-224 1727 atoms, 1770 bonds, 1 pseudobond, 223 residues, 2 models selected > hide sel atoms > hide sel cartoons > select /F:1-397 2993 atoms, 3072 bonds, 2 pseudobonds, 378 residues, 2 models selected > select /E:1-395 2902 atoms, 2977 bonds, 3 pseudobonds, 368 residues, 2 models selected > hide sel cartoons Drag select of 173 residues > color sel green > select /F:265 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 255 atoms, 256 bonds, 31 residues, 1 model selected > color sel green > select clear > select /F:241 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 26 atoms, 27 bonds, 3 residues, 1 model selected > select up 2993 atoms, 3072 bonds, 378 residues, 1 model selected > select down 26 atoms, 27 bonds, 3 residues, 1 model selected > select clear Drag select of 61 residues > select up 922 atoms, 935 bonds, 116 residues, 1 model selected > select down 480 atoms, 61 residues, 1 model selected > color sel blue > select clear > select /F:41 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 77 atoms, 78 bonds, 9 residues, 1 model selected > color sel blue > select clear > select /F:203 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 48 atoms, 47 bonds, 7 residues, 1 model selected > color sel blue > select /F:209 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 22 atoms, 22 bonds, 3 residues, 1 model selected > select up 2993 atoms, 3072 bonds, 378 residues, 1 model selected > select down 22 atoms, 22 bonds, 3 residues, 1 model selected > color sel blue > select /F:218 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel blue > select /F:220 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 26 atoms, 25 bonds, 4 residues, 1 model selected > color sel blue > select /F:196 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 72 atoms, 72 bonds, 9 residues, 1 model selected > color sel blue > select /F:211 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 40 atoms, 39 bonds, 5 residues, 1 model selected > color sel blue > select /F:217 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 27 atoms, 27 bonds, 3 residues, 1 model selected > color sel blue > select /F:37 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel blue > select /F:254 7 atoms, 7 bonds, 1 residue, 1 model selected > color sel blue > select /F:229 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 10 atoms, 9 bonds, 2 residues, 1 model selected > color sel blue > select clear Drag select of 113 residues, 1 pseudobonds > color sel red > select clear > select /F:144 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 36 atoms, 37 bonds, 4 residues, 1 model selected > color sel red > select clear > movie record > turn y 2 180 > wait 180 > enocde Unknown command: movie enocde > movie record Already recording a movie > movie encode Movie saved to /Users/laotangmu233/Desktop/movie.mp4 > open 6LGX Summary of feedback from opening 6LGX fetched from pdb --- note | Fetching compressed mmCIF 6lgx from http://files.rcsb.org/download/6lgx.cif 6lgx title: Structure of Rabies virus glycoprotein at basic pH [more info...] Chain information for 6lgx #2 --- Chain | Description | UniProt A B | Glycoprotein,Glycoprotein,Glycoprotein | Q5JZZ2_9RHAB 1-74, Q2Z2I1_9RHAB 80-120, D8VEC1_9RHAB 126-439 6lgx mmCIF Assemblies --- 1| author_and_software_defined_assembly > hide #!1 models > show #!1 models > hide #!1 models > select #2/B:2-408 2727 atoms, 2802 bonds, 3 pseudobonds, 348 residues, 2 models selected > select #2/A:1-419 2968 atoms, 3048 bonds, 3 pseudobonds, 377 residues, 2 models selected > hide sel cartoons > show #!1 models > hide #!1 models > select #2/A:1-419 2968 atoms, 3048 bonds, 3 pseudobonds, 377 residues, 2 models selected > select #2/B:2-408 2727 atoms, 2802 bonds, 3 pseudobonds, 348 residues, 2 models selected > select clear > select #2/B:395 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 144 atoms, 148 bonds, 19 residues, 1 model selected > select up 2727 atoms, 2802 bonds, 348 residues, 1 model selected > select down 144 atoms, 148 bonds, 19 residues, 1 model selected > select clear Drag select of 113 residues > select clear Drag select of 21 residues > color green > select clear Drag select of 46 residues > select clear Drag select of 49 residues > color blue > undo > show #!1 models > hide #!1 models > select clear Drag select of 157 residues, 1 pseudobonds > color sel green > select #2/B:294 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 127 atoms, 126 bonds, 16 residues, 1 model selected > color sel green > select #2/B:320 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 17 atoms, 16 bonds, 2 residues, 1 model selected > color sel green > select clear > select #2/B:12 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel green > select clear Drag select of 72 residues > select up 692 atoms, 703 bonds, 90 residues, 1 model selected > select down 557 atoms, 72 residues, 1 model selected > color sel blue > select #2/B:32 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 122 atoms, 122 bonds, 17 residues, 1 model selected > select down 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel blue > select clear > select #2/B:33 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel blue > select #2/B:228 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel blue > select clear > select #2/B:253 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 126 atoms, 128 bonds, 16 residues, 1 model selected > select down 7 atoms, 7 bonds, 1 residue, 1 model selected > select clear Drag select of 13 residues > color sel blue > select #2/B:215 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel blue Drag select of 86 residues, 2 pseudobonds > color sel red > select #2/B:153 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 185 atoms, 189 bonds, 25 residues, 1 model selected > color sel red > select #2/B:146 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 50 atoms, 51 bonds, 6 residues, 1 model selected > color sel red > select #2/B:187 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 89 atoms, 91 bonds, 11 residues, 1 model selected > color sel red > select #2/B:54 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel red > select clear > show #!1 models > matchmaker 6lgw to 6lgx Missing or invalid ""matchAtoms"" argument: invalid atoms specifier > matchmaker #6lgw to #6lgx Missing or invalid ""matchAtoms"" argument: only initial part ""#6"" of atom specifier valid > 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 6lgx, chain A (#2) with 6lgw, chain F (#1), sequence alignment score = 1971.4 RMSD between 23 pruned atom pairs is 1.228 angstroms; (across all 355 pairs: 33.765) > matchmaker #1:262-390 to #2:262-390 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 6lgx, chain A (#2) with 6lgw, chain F (#1), sequence alignment score = 598.6 RMSD between 96 pruned atom pairs is 0.747 angstroms; (across all 121 pairs: 3.732) > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > mmaker #1:1-190 to #2:1-190 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 6lgx, chain A (#2) with 6lgw, chain F (#1), sequence alignment score = 818.5 RMSD between 94 pruned atom pairs is 0.649 angstroms; (across all 162 pairs: 26.177) > save ""/Users/laotangmu233/Desktop/matchermarker two proteins.cxs"" > ui tool show Matchmaker > select ~sel & ##selected Nothing selected > mmaker #1/B:1-190 to #2/F:1-190 No 'to' model specified > mmaker #1/B to #2/F No 'to' model specified > mmaker #2/F to #1/B No 'to' model specified > mmaker #2/F #1/B > matchmaker #2/F #1/B Missing required ""to"" argument > mmaker #2/F to #1/B No 'to' model specified > ui tool show Matchmaker > matchmaker #!2 to #1/E pairing bs Parameters --- Chain pairing | bs 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 6lgw, chain E (#1) with 6lgx, chain A (#2), sequence alignment score = 1895.2 RMSD between 31 pruned atom pairs is 0.647 angstroms; (across all 350 pairs: 41.759) > hide #!1 models > select #2 5695 atoms, 5850 bonds, 6 pseudobonds, 725 residues, 2 models selected > show cartoons > select #1 9342 atoms, 9582 bonds, 7 pseudobonds, 1191 residues, 2 models selected > show sel cartoons > show #!1 models > hide #!2 models > open 6lgx 6lgx title: Structure of Rabies virus glycoprotein at basic pH [more info...] Chain information for 6lgx #3 --- Chain | Description | UniProt A B | Glycoprotein,Glycoprotein,Glycoprotein | Q5JZZ2_9RHAB 1-74, Q2Z2I1_9RHAB 80-120, D8VEC1_9RHAB 126-439 6lgx mmCIF Assemblies --- 1| author_and_software_defined_assembly > mmaker #3 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 6lgw, chain F (#1) with 6lgx, chain A (#3), sequence alignment score = 1971.4 RMSD between 23 pruned atom pairs is 1.228 angstroms; (across all 355 pairs: 33.765) > hide #!1 models > show #!1 models > select #3/B 2727 atoms, 2802 bonds, 3 pseudobonds, 348 residues, 2 models selected > hide sel cartoons > hide #!3 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/E #1/F Alignment identifier is 1 > select > #1/E-F:5-11,15-16,37-46,55-69,81-87,127-143,148-150,158-159,169-170,176-180,192-201,206-210,216-218,223-227,230-234,240-242,310-318,321-332,346-347,350-351,364-365,371-372 2058 atoms, 2064 bonds, 260 residues, 1 model selected > show #!3 models > open /Users/laotangmu233/Desktop/test.rtf Unrecognized file suffix '.rtf' > open /Users/laotangmu233/Desktop/test.cxc > {\rtf1\ansi\ansicpg1252\cocoartf2757 Unknown command: {\rtf1\ansi\ansicpg1252\cocoartf2757 > open /Users/laotangmu233/Desktop/test.cxc > {\rtf1\ansi\ansicpg1252\cocoartf2757 Failed opening file /Users/laotangmu233/Desktop/test.cxc: Unknown command: {\rtf1\ansi\ansicpg1252\cocoartf2757 > open /Users/laotangmu233/Downloads/6lgx.pdb 6lgx.pdb title: Structure of rabies virus glycoprotein At basic pH [more info...] Chain information for 6lgx.pdb #4 --- Chain | Description | UniProt A B | glycoprotein,glycoprotein,glycoprotein | Q5JZZ2_9RHAB 1-74, Q2Z2I1_9RHAB 80-120, D8VEC1_9RHAB 126-439 > open /Users/laotangmu233/Desktop/chimera_script.cxc > Open 6lgw Unknown command: Open 6lgw > save /Users/laotangmu233/Desktop/MM.cxs > close > open /Users/laotangmu233/Desktop/MM.cxs format session ===== 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 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-22.1.27 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel 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 Air Model Identifier: MacBookAir9,1 Processor Name: Quad-Core Intel Core i5 Processor Speed: 1.1 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 2020.0.1.0.0 (iBridge: 21.16.365.0.0,0) OS Loader Version: 580~439 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 56 days, 2 hours, 30 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a51 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 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: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 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 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 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: 1.5.13 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: 1.0.3 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: 1.12.3 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: 2.2.2 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: 1.33.2 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: 0.2.0 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: 4.47.0 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: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 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: 10.0.1 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: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 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: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX