id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16121 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.5-arm64-arm-64bit ChimeraX Version: 1.8rc202405171936 (2024-05-17 19:36:10 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 0x0000000205764c00 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 63 in update File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 19 in __init__ File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 90 in copy File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 642 in _try File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 137 in __enter__ File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 665 in _option File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 137 in __enter__ File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 439 in _atom_ File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 396 in block7 File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 787 in _positive_closure File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 398 in _residue_ File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 344 in block2 File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 771 in _closure File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 346 in _chain_ File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 323 in block0 File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 748 in _repeater File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 789 in _positive_closure File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 325 in _model_parts_ File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 200 in _model_ File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 157 in block0 File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 787 in _positive_closure File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 159 in _model_list_ File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 136 in _as_term_ File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 89 in _atom_specifier_ File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 206 in parse File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 192 in _parse_unquoted File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 121 in parse File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py"", line 123 in parse File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2780 in _parse_arg File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2926 in _process_positional_arguments File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3166 in run File ""/Applications/ChimeraX-1.8-rc2024.05.17.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-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/show_sequences/tool.py"", line 74 in show_seqs File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 285 in event_loop File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1006 in init File ""/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1169 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, lxml._elementpath, lxml.etree, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 55) {""app_name"":""ChimeraX"",""timestamp"":""2024-10-11 13:37:02.00 -0500"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.5 (23F79)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""EFC7D5D0-1426-4D2E-8BC3-AE3C7A16AD6F""} { ""uptime"" : 6600, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac15,6"", ""coalitionID"" : 3619, 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\nSTACK GUARD 832K 52 \nStack 177.8M 53 \nStack Guard 56.0M 1 \nVM_ALLOCATE 256.2M 166 \nVM_ALLOCATE (reserved) 224.0M 3 reserved VM address space (unallocated)\n__AUTH 1864K 373 \n__AUTH_CONST 29.6M 585 \n__CTF 824 1 \n__DATA 21.3M 731 \n__DATA_CONST 40.1M 740 \n__DATA_DIRTY 1872K 222 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 562.6M 150 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2199K 1 \n__TEXT 901.0M 757 \ndyld private memory 592K 6 \nmapped file 229.3M 57 \nshared memory 3264K 23 \n=========== ======= ======= \nTOTAL 4.7G 4168 \nTOTAL, minus reserved VM space 4.5G 4168 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""ac459ddd46731b6d5108760bd043bcdc617e719f"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6297d96be2c9387df974efa4"", ""factorPackIds"" : { }, ""deploymentId"" : 240000032 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 }, { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8rc202405170741 (2024-05-17) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/maryam/Downloads/9ayf.pdb 9ayf.pdb title: Structure of human calcium-sensing receptor In complex with GI1 (MINIGI1) protein In detergent [more info...] Chain information for 9ayf.pdb #1 --- Chain | Description | UniProt A | adenylate cyclase-inhibiting G α protein | GNAI1_HUMAN 1-57 66-229 B | transducin β chain 1 | GBB1_HUMAN 2-340 G | G γ-I | GBG2_HUMAN 1-71 H | single-chain antibody fragment SCFV16 | Q R | isoform 1 of extracellular calcium-sensing receptor | CASR_HUMAN -7-903 Non-standard residues in 9ayf.pdb #1 --- 9IG — 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine AV0 — lauryl maltose neopentyl glycol (2,2-didecylpropane-1,3-bis-B-D- maltopyranoside; 2-decyl-2-{[(4-O-α-D-glucopyranosyl-β-D- glucopyranosyl)oxy]methyl}DODECYL4-O-α-D-glucopyranosyl-β-D-glucopyranoside) CA — calcium ion NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) PO4 — phosphate ion TCR — cyclomethyltryptophan > hide atoms > show atoms > show cartoons > style stick Changed 19630 atom styles > hide cartoons > show cartoons > hide atoms > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > ui tool show ""Show Sequence Viewer"" > sequence chain /G Alignment identifier is 1/G > select clear > select /G 447 atoms, 453 bonds, 58 residues, 1 model selected > delete :1-51 > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > delete :7-293 > ui tool show ""Show Sequence Viewer"" > close #1 > open /Users/maryam/Downloads/9ayf.pdb format pdb 9ayf.pdb title: Structure of human calcium-sensing receptor In complex with GI1 (MINIGI1) protein In detergent [more info...] Chain information for 9ayf.pdb #1 --- Chain | Description | UniProt A | adenylate cyclase-inhibiting G α protein | GNAI1_HUMAN 1-57 66-229 B | transducin β chain 1 | GBB1_HUMAN 2-340 G | G γ-I | GBG2_HUMAN 1-71 H | single-chain antibody fragment SCFV16 | Q R | isoform 1 of extracellular calcium-sensing receptor | CASR_HUMAN -7-903 Non-standard residues in 9ayf.pdb #1 --- 9IG — 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine AV0 — lauryl maltose neopentyl glycol (2,2-didecylpropane-1,3-bis-B-D- maltopyranoside; 2-decyl-2-{[(4-O-α-D-glucopyranosyl-β-D- glucopyranosyl)oxy]methyl}DODECYL4-O-α-D-glucopyranosyl-β-D-glucopyranoside) CA — calcium ion NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) PO4 — phosphate ion TCR — cyclomethyltryptophan > show cartoons > show atoms > hide atoms > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > delete :7-293 > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > ui tool show ""Show Sequence Viewer"" ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8rc202405170741 (2024-05-17) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,6 Model Number: Z1AX00298LL/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 2 hours, 59 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57 ChimeraX-AtomicLibrary: 14.0.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.4 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.4 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: 1.8rc202405170741 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.3 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.4 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.3 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.51.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.2 typing-extensions: 4.11.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX