id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16439 Crash in python_instances_of_class chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.2-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00000001e4280100 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 52 in File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 61 in File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 61 in python_instances_of_class File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 176 in _copy_custom_attrs File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 162 in copy File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py"", line 65 in combine_cmd File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3213 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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, 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""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"", ""CFBundleVersion"" : ""1953.300"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6589472768, ""size"" : 421876, ""uuid"" : ""e2679357-b2af-30d4-8130-50d31765af88"", ""path"" : ""\/usr\/lib\/libc++.1.dylib"", ""name"" : ""libc++.1.dylib"" } ], ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=3.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 9408K 8 \nCG image 3360K 47 \nColorSync 592K 29 \nCoreAnimation 5376K 30 \nCoreGraphics 64K 4 \nCoreUI image data 5248K 37 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 1.5G 258 \nMALLOC guard page 192K 10 \nMALLOC_MEDIUM (reserved) 1.2G 12 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 896K 56 \nStack 179.9M 57 \nStack Guard 56.0M 1 \nVM_ALLOCATE 272.1M 233 \nVM_ALLOCATE (reserved) 288.0M 4 reserved VM address space (unallocated)\n__AUTH 1972K 371 \n__AUTH_CONST 25.2M 601 \n__CTF 756 1 \n__DATA 20.5M 748 \n__DATA_CONST 38.7M 753 \n__DATA_DIRTY 2031K 238 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 796.5M 151 \n__OBJC_CONST 4898K 338 \n__OBJC_RO 65.5M 1 \n__OBJC_RW 1988K 1 \n__TEXT 846.7M 774 \ndyld private memory 256K 1 \nmapped file 214.8M 58 \nshared memory 3232K 30 \n=========== ======= ======= \nTOTAL 5.5G 4867 \nTOTAL, minus reserved VM space 4.0G 4867 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""62cdf63ddb3b7109d6d765cc"", ""factorPackIds"" : { ""SIRI_UNDERSTANDING_TMDC"" : ""62cdf6dddb3b7109d6d765cd"" }, ""deploymentId"" : 240000007 } ], ""experiments"" : [ { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/andydelaitsch/Documents/bjorklab/007/EM_maps_final/0_Fabs/BG505DS_linear_1_007_linear_fixed2_glycans.pdb Summary of feedback from opening /Users/andydelaitsch/Documents/bjorklab/007/EM_maps_final/0_Fabs/BG505DS_linear_1_007_linear_fixed2_glycans.pdb --- warnings | Cannot find LINK/SSBOND residue MAN (531 ) Cannot find LINK/SSBOND residue NAG (535 ) Cannot find LINK/SSBOND residue MAN (505 ) Cannot find LINK/SSBOND residue NAG (535 ) Cannot find LINK/SSBOND residue NAG (535 ) 48 messages similar to the above omitted Chain information for BG505DS_linear_1_007_linear_fixed2_glycans.pdb #1 --- Chain | Description A | No description available A | No description available B D F | No description available C E | No description available C E | No description available H | No description available L | No description available > open > /Users/andydelaitsch/Documents/bjorklab/007/EM_maps_final/0_Fabs/0_bound_cryosparc_P78_J197_006_volume_map_sharp_zflip.mrc Opened 0_bound_cryosparc_P78_J197_006_volume_map_sharp_zflip.mrc as #2, grid size 392,392,392, pixel 0.832, shown at level 0.0687, step 2, values float32 > volume #2 step 1 > volume #2 level 0.2274 > show cartoons > hide atoms > hide #!2 models > dssp #1 > show #!2 models > select /L:86 12 atoms, 12 bonds, 1 residue, 1 model selected > select add /H:37 20 atoms, 19 bonds, 2 residues, 1 model selected > select up 121 atoms, 126 bonds, 13 residues, 1 model selected > select up 1791 atoms, 1837 bonds, 234 residues, 1 model selected > select up 15902 atoms, 16246 bonds, 1967 residues, 1 model selected > select down 1791 atoms, 1837 bonds, 234 residues, 1 model selected > delete sel > transparency #2 50 > lighting soft > set bgColor white > graphics silhouettes true > select add #1 14111 atoms, 14409 bonds, 27 pseudobonds, 1733 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.68014,0.31373,0.66256,-119.13,-0.636,0.702,0.32047,92.463,-0.36458,-0.63935,0.67699,220.4 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.68014,0.31373,0.66256,-115.08,-0.636,0.702,0.32047,90.952,-0.36458,-0.63935,0.67699,210.08 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.73322,0.24932,0.63263,-107.63,-0.56932,0.73382,0.37065,66.147,-0.37183,-0.63194,0.68,209.48 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.73322,0.24932,0.63263,-104.47,-0.56932,0.73382,0.37065,71.66,-0.37183,-0.63194,0.68,209.03 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.78522,0.34205,0.51617,-107.02,-0.56034,0.74726,0.35723,70.439,-0.26352,-0.56974,0.77843,163.98 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.78522,0.34205,0.51617,-108.91,-0.56034,0.74726,0.35723,70.171,-0.26352,-0.56974,0.77843,163.05 Must specify one map, got 0 > fitmap #1 inMap #2 Fit molecule BG505DS_linear_1_007_linear_fixed2_glycans.pdb (#1) to map 0_bound_cryosparc_P78_J197_006_volume_map_sharp_zflip.mrc (#2) using 14111 atoms average map value = 0.4859, steps = 92 shifted from previous position = 2.08 rotated from previous position = 7.92 degrees atoms outside contour = 3323, contour level = 0.22741 Position of BG505DS_linear_1_007_linear_fixed2_glycans.pdb (#1) relative to 0_bound_cryosparc_P78_J197_006_volume_map_sharp_zflip.mrc (#2) coordinates: Matrix rotation and translation 0.77278079 0.40446028 0.48910299 -114.24406224 -0.61686336 0.65993331 0.42891447 80.96326031 -0.14929648 -0.63316658 0.75948051 158.63138869 Axis -0.66139302 0.39755248 -0.63601203 Axis point 0.00000000 251.09091815 16.66993780 Rotation angle (degrees) 53.40910407 Shift along axis 6.85589807 > select clear > open > /Users/andydelaitsch/Documents/bjorklab/007/EM_maps_final/0_Fabs/BG505DS_linear_1_007_linear_fixed2_glycans.pdb Summary of feedback from opening /Users/andydelaitsch/Documents/bjorklab/007/EM_maps_final/0_Fabs/BG505DS_linear_1_007_linear_fixed2_glycans.pdb --- warnings | Cannot find LINK/SSBOND residue MAN (531 ) Cannot find LINK/SSBOND residue NAG (535 ) Cannot find LINK/SSBOND residue MAN (505 ) Cannot find LINK/SSBOND residue NAG (535 ) Cannot find LINK/SSBOND residue NAG (535 ) 48 messages similar to the above omitted Chain information for BG505DS_linear_1_007_linear_fixed2_glycans.pdb #3 --- Chain | Description A | No description available A | No description available B D F | No description available C E | No description available C E | No description available H | No description available L | No description available > select #3/C 3681 atoms, 3758 bonds, 8 pseudobonds, 452 residues, 2 models selected > select ~sel & ##selected 12221 atoms, 12488 bonds, 19 pseudobonds, 1515 residues, 2 models selected > delete sel > ui tool show Matchmaker > matchmaker #!3 to #1/A pairing bs Specify a single 'to' chain only > ui tool show Matchmaker > matchmaker #!3 to #1/A pairing bs Specify a single 'to' chain only > ui tool show Matchmaker > matchmaker #!3 to #1/A pairing bs Specify a single 'to' chain only > save > /Users/andydelaitsch/Documents/bjorklab/007/EM_maps_final/0_Fabs/protomerC_linear.pdb > models #3 > open > /Users/andydelaitsch/Documents/bjorklab/007/EM_maps_final/0_Fabs/protomerC_linear.pdb Chain information for protomerC_linear.pdb #4 --- Chain | Description C | No description available > close #3 > ui tool show Matchmaker > hide #!1 models > show #!1 models > select #1/A:461 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 25 atoms, 23 bonds, 4 residues, 1 model selected > select up 717 atoms, 729 bonds, 90 residues, 1 model selected > select up 731 atoms, 742 bonds, 92 residues, 1 model selected > select up 2322 atoms, 2367 bonds, 299 residues, 1 model selected > select up 2338 atoms, 2382 bonds, 301 residues, 1 model selected > select up 3112 atoms, 3170 bonds, 394 residues, 1 model selected > select up 3147 atoms, 3205 bonds, 399 residues, 1 model selected > select up 3417 atoms, 3487 bonds, 432 residues, 1 model selected > select up 3782 atoms, 3865 bonds, 460 residues, 1 model selected > select up 14111 atoms, 14409 bonds, 1733 residues, 1 model selected > select down 3782 atoms, 3865 bonds, 460 residues, 1 model selected > ui tool show Matchmaker > matchmaker #!4 to #1 & sel 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 BG505DS_linear_1_007_linear_fixed2_glycans.pdb, chain A (#1) with protomerC_linear.pdb, chain C (#4), sequence alignment score = 2136.4 RMSD between 419 pruned atom pairs is 0.393 angstroms; (across all 431 pairs: 0.896) > matchmaker #!4 to #1 & sel 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 BG505DS_linear_1_007_linear_fixed2_glycans.pdb, chain A (#1) with protomerC_linear.pdb, chain C (#4), sequence alignment score = 2136.4 RMSD between 419 pruned atom pairs is 0.393 angstroms; (across all 431 pairs: 0.896) > hide #!2 models > hide #!4 models > delete sel > show #!4 models > select #4/C:109 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 141 atoms, 143 bonds, 17 residues, 1 model selected > select down 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 141 atoms, 143 bonds, 17 residues, 1 model selected > select up 791 atoms, 804 bonds, 96 residues, 1 model selected > select up 981 atoms, 998 bonds, 121 residues, 1 model selected > select up 2701 atoms, 2759 bonds, 343 residues, 1 model selected > select up 2717 atoms, 2774 bonds, 345 residues, 1 model selected > select up 3075 atoms, 3138 bonds, 391 residues, 1 model selected > select up 3088 atoms, 3150 bonds, 393 residues, 1 model selected > select up 3418 atoms, 3488 bonds, 433 residues, 1 model selected > select up 3681 atoms, 3758 bonds, 452 residues, 1 model selected > select up 14010 atoms, 14302 bonds, 1725 residues, 4 models selected > select down 3681 atoms, 3758 bonds, 452 residues, 1 model selected > ui tool show ""Change Chain IDs"" > changechains sel A Chain IDs of 452 residues changed > changechains sel A Chain IDs of 0 residues changed > combine #1, 4 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M2 Max 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: Mac14,6 Model Number: MNWA3LL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 8419.80.7 OS Loader Version: 8419.80.7 Software: System Software Overview: System Version: macOS 13.2 (22D49) Kernel Version: Darwin 22.3.0 Time since boot: 19 days, 22 hours, 41 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 38 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG UltraFine: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes 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: 1.6.4 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: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 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: 1.2.7 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: 1.0.5 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: 1.8 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: 1.2.4 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: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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: 1.13.5 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: 3.0.15 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: 1.16.5 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: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 4.53.0 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: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 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: 3.0.47 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: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX