id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14523 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.6.5-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 Thread 0x0000700012375000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001103bf600 (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/numpy/core/_internal.py"", line 255 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 333 in pointer File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 251 in set_cvec_pointer File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 133 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 1022 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 83 in _elements File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 209 in get_prop File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py"", line 185 in template_residue_name File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py"", line 147 in check_residues File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py"", line 41 in assign_charges File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py"", line 99 in cmd_coulombic 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/shortcuts/shortcuts.py"", line 525 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 582 in run_expanded_command File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 72 in func_plus_tip File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 339 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 420 in run_shortcut File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 402 in try_shortcut File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 1376 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py"", line 66 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1302 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py"", line 397 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py"", line 205 in callback 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, 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""rolloutId"" : ""607844aa04477260f58a8077"", ""factorPackIds"" : { ""SIRI_MORPHUN_ASSETS"" : ""6103050cbfe6dc472e1c982a"" }, ""deploymentId"" : 240000066 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== 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 2GTL format mmcif fromDatabase pdb 2gtl title: Lumbricus Erythrocruorin at 3.5A resolution [more info...] Chain information for 2gtl #1 --- Chain | Description | UniProt A E I | Extracellular globin 4 | GLB4_LUMTE 1-151 B F J | Extracellular globin 2 | GLB2_LUMTE 1-145 C G K | Extracellular globin-3 | GLB3_LUMTE 1-153 D H L | Hemoglobin chain d1 | O61233_LUMTE 8-147 M | Hemoglobin linker chain L1 | Q9GV76_LUMTE 9-225 N | Extracellular hemoglobin linker L2 subunit | Q2I743_LUMTE 10-229 O | Extracellular hemoglobin linker L3 subunit | Q2I742_LUMTE 8-222 Non-standard residues in 2gtl #1 --- CA — calcium ion CMO — carbon monoxide HEM — protoporphyrin IX containing Fe (HEME) ZN — zinc ion 2gtl mmCIF Assemblies --- 1| complete point assembly 2| point asymmetric unit 3| point asymmetric unit, std point frame 4| crystal asymmetric unit > select /M /N /O 5095 atoms, 5210 bonds, 19 pseudobonds, 657 residues, 2 models selected > select ~sel & ##selected 14553 atoms, 14925 bonds, 88 pseudobonds, 1767 residues, 2 models selected > hide sel atoms > select ~sel & ##selected 5095 atoms, 5210 bonds, 19 pseudobonds, 657 residues, 2 models selected > hide sel atoms > show sel cartoons > mlp sel Map values for surface ""2gtl_M SES surface"": minimum -27.51, mean -4.23, maximum 21.91 Map values for surface ""2gtl_N SES surface"": minimum -28.72, mean -4.949, maximum 21.91 Map values for surface ""2gtl_O SES surface"": minimum -29, mean -5.716, maximum 22.98 To also show corresponding color key, enter the above mlp command and add key true > hide sel surfaces > select clear > select add /M:26 5 atoms, 4 bonds, 1 residue, 1 model selected > select add /N:24 13 atoms, 11 bonds, 2 residues, 2 models selected > select add /O:27 19 atoms, 16 bonds, 3 residues, 3 models selected > select up 597 atoms, 600 bonds, 79 residues, 4 models selected > show sel atoms > style sel stick Changed 597 atom styles > color sel byhetero > coulombic sel The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /M LEU 13 /M LYS 15 /M ASP 22 /M LYS 26 /M LYS 27 /M ASP 30 /M LYS 37 /M ASP 43 /M LYS 44 /M LYS 45 /M GLU 59 /M GLU 64 /M SER 187 /N PHE 19 /N ARG 23 /N ARG 26 /N GLU 39 /N ASP 186 /N HIS 228 /N ASP 229 /O GLN 8 /O SER 9 /O HIS 10 /O ASP 11 /O GLU 12 /O ILE 13 /O ILE 14 /O ASP 15 /O LYS 16 /O LEU 17 /O ILE 18 /O GLU 19 /O LYS 23 /O LYS 221 /O LYS 222 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 2gtl_M SES surface #1.2: minimum, -25.60, mean -4.72, maximum 12.62 Coulombic values for 2gtl_N SES surface #1.3: minimum, -23.87, mean -3.44, maximum 16.59 Coulombic values for 2gtl_O SES surface #1.4: minimum, -45.36, mean -7.97, maximum 10.68 To also show corresponding color key, enter the above coulombic command and add key true > undo > hide sel surfaces > style sel stick Changed 597 atom styles > color sel byhetero > select clear > lighting soft > lighting simple > lighting full > set bgColor black > set bgColor white > lighting simple > lighting soft > set bgColor black > mlp Map values for surface ""2gtl_A SES surface"": minimum -27.35, mean -3.46, maximum 25.63 Map values for surface ""2gtl_B SES surface"": minimum -24.43, mean -4.748, maximum 23.49 Map values for surface ""2gtl_C SES surface"": minimum -29.2, mean -4.082, maximum 25.1 Map values for surface ""2gtl_D SES surface"": minimum -27.96, mean -3.691, maximum 23.3 Map values for surface ""2gtl_E SES surface"": minimum -27.49, mean -3.405, maximum 25.96 Map values for surface ""2gtl_F SES surface"": minimum -25.45, mean -4.776, maximum 24.49 Map values for surface ""2gtl_G SES surface"": minimum -28.11, mean -4.069, maximum 24.69 Map values for surface ""2gtl_H SES surface"": minimum -28.09, mean -3.677, maximum 23.35 Map values for surface ""2gtl_I SES surface"": minimum -27.61, mean -3.48, maximum 26.12 Map values for surface ""2gtl_J SES surface"": minimum -25.38, mean -4.745, maximum 24.81 Map values for surface ""2gtl_K SES surface"": minimum -30.19, mean -4.019, maximum 24.42 Map values for surface ""2gtl_L SES surface"": minimum -29.02, mean -3.7, maximum 22.67 Map values for surface ""2gtl_M SES surface"": minimum -27.51, mean -4.23, maximum 21.91 Map values for surface ""2gtl_N SES surface"": minimum -28.72, mean -4.949, maximum 21.91 Map values for surface ""2gtl_O SES surface"": minimum -29, mean -5.716, maximum 22.98 To also show corresponding color key, enter the above mlp command and add key true > color byhetero > hide surfaces > select /A:5-151 1209 atoms, 1238 bonds, 147 residues, 1 model selected > select :HEM 516 atoms, 552 bonds, 48 pseudobonds, 12 residues, 2 models selected > show sel atoms > select clear > select /G:160@FE 1 atom, 1 residue, 1 model selected > select up 43 atoms, 46 bonds, 1 residue, 1 model selected > select up 1230 atoms, 1257 bonds, 151 residues, 1 model selected > show sel cartoons > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 43 atoms, 46 bonds, 1 residue, 1 model selected > select up 1193 atoms, 1224 bonds, 147 residues, 1 model selected > show sel cartoons > save /Users/annahorton/Desktop/image1.png supersample 3 > mlp sel Map values for surface ""2gtl_F SES surface"": minimum -25.45, mean -4.776, maximum 24.49 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface ""2gtl_F SES surface"": minimum -25.45, mean -4.776, maximum 24.49 To also show corresponding color key, enter the above mlp command and add key true > show sel surfaces > mlp sel Map values for surface ""2gtl_F SES surface"": minimum -25.45, mean -4.776, maximum 24.49 To also show corresponding color key, enter the above mlp command and add key true > close session > open 2GTL format mmcif fromDatabase pdb 2gtl title: Lumbricus Erythrocruorin at 3.5A resolution [more info...] Chain information for 2gtl #1 --- Chain | Description | UniProt A E I | Extracellular globin 4 | GLB4_LUMTE 1-151 B F J | Extracellular globin 2 | GLB2_LUMTE 1-145 C G K | Extracellular globin-3 | GLB3_LUMTE 1-153 D H L | Hemoglobin chain d1 | O61233_LUMTE 8-147 M | Hemoglobin linker chain L1 | Q9GV76_LUMTE 9-225 N | Extracellular hemoglobin linker L2 subunit | Q2I743_LUMTE 10-229 O | Extracellular hemoglobin linker L3 subunit | Q2I742_LUMTE 8-222 Non-standard residues in 2gtl #1 --- CA — calcium ion CMO — carbon monoxide HEM — protoporphyrin IX containing Fe (HEME) ZN — zinc ion 2gtl mmCIF Assemblies --- 1| complete point assembly 2| point asymmetric unit 3| point asymmetric unit, std point frame 4| crystal asymmetric unit > select /M:9-225 1705 atoms, 1750 bonds, 217 residues, 1 model selected > select /M /N /O 5095 atoms, 5210 bonds, 19 pseudobonds, 657 residues, 2 models selected > select ~sel & ##selected 14553 atoms, 14925 bonds, 88 pseudobonds, 1767 residues, 2 models selected > select /M:9-225 1705 atoms, 1750 bonds, 217 residues, 1 model selected > select /M /N /O 5095 atoms, 5210 bonds, 19 pseudobonds, 657 residues, 2 models selected > select ~sel & ##selected 14553 atoms, 14925 bonds, 88 pseudobonds, 1767 residues, 2 models selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select /M:9-225 1705 atoms, 1750 bonds, 217 residues, 1 model selected > select /N:10-229 1722 atoms, 1757 bonds, 220 residues, 1 model selected > select /M:9-225 1705 atoms, 1750 bonds, 217 residues, 1 model selected > select /M /N /O 5095 atoms, 5210 bonds, 19 pseudobonds, 657 residues, 2 models selected > style sel stick Changed 5095 atom styles > style sel ball Changed 5095 atom styles > style sel stick Changed 5095 atom styles > show sel cartoons > mlp sel Map values for surface ""2gtl_M SES surface"": minimum -27.51, mean -4.23, maximum 21.91 Map values for surface ""2gtl_N SES surface"": minimum -28.72, mean -4.949, maximum 21.91 Map values for surface ""2gtl_O SES surface"": minimum -29, mean -5.716, maximum 22.98 To also show corresponding color key, enter the above mlp command and add key true > select clear > hide surfaces > coulombic ===== Log before crash end ===== Log: 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-18.8.6 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine (1x6x8 (fused) LP 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: Dual-Core Intel Core i3 Processor Speed: 1.1 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 512 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0) OS Loader Version: 540.120.3~22 Software: System Software Overview: System Version: macOS 12.6.5 (21G531) Kernel Version: Darwin 21.6.0 Time since boot: 25 days 5:35 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: 0x8a5c Revision ID: 0x0007 Metal Family: Supported, Metal GPUFamily macOS 2 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 can't reproduce Tom Goddard all ChimeraX