id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17103 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-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 0x0000000202e3d240 (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 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""/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/gui.py"", line 1977 in _open_dropped_file File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 240 in event 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 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bundle 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/enniodamico/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Desktop/All data/Stamps > project/Rab11FIP3/R11F3-pointed-withadaptor-fitted-inj007.pdb"" Chain information for R11F3-pointed-withadaptor-fitted-inj007.pdb #1 --- Chain | Description A | No description available B | No description available I | No description available J | No description available U | No description available W | No description available Y | No description available > show atoms > show cartoons > style stick Changed 23394 atom styles > contacts /C-Z restrict /A-B distanceOnly 4.0 select true 709 distances > select up 835 atoms, 807 bonds, 66 residues, 1 model selected > select ~sel 22559 atoms, 22758 bonds, 1520 residues, 1 model selected > hide sel atoms > select ~sel 835 atoms, 807 bonds, 709 pseudobonds, 66 residues, 2 models selected > color sel byhetero > open ""/Users/enniodamico/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Desktop/All data/Stamps project/00-Paper- > FinalData/Figures/Ninein/Ninein-PE.cxs"" Opened 042-PointedEnd.mrc as #1, grid size 300,300,300, pixel 1.3, shown at level 0.01, step 1, values float32 Opened 042-PointedEnd.mrc 0 as #4.1, grid size 300,300,300, pixel 1.3, shown at level 0.0124, step 1, values float32 Opened 042-PointedEnd.mrc 1 as #4.2, grid size 300,300,300, pixel 1.3, shown at level 0.01, step 1, values float32 Opened 042-PointedEnd.mrc 2 as #4.3, grid size 300,300,300, pixel 1.3, shown at level 0.01, step 1, values float32 Opened 042-PointedEnd.mrc 3 as #4.4, grid size 300,300,300, pixel 1.3, shown at level 0.01, step 1, values float32 Opened 042-PointedEnd.mrc 4 as #4.5, grid size 300,300,300, pixel 1.3, shown at level 0.01, step 1, values float32 Opened 042-PointedEnd.mrc 5 as #4.6, grid size 300,300,300, pixel 1.3, shown at level 0.01, step 1, values float32 opened ChimeraX session > ui tool show ""Show Sequence Viewer"" > sequence chain #2/1 Alignment identifier is 2/1 > sequence chain #2/2 Alignment identifier is 2/2 > select #2/2:551-552 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2/2:551-561 94 atoms, 94 bonds, 11 residues, 1 model selected > select #2/1:545 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/1:527-560,605-629 465 atoms, 465 bonds, 59 residues, 1 model selected > select #2/1:549 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/1:549 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/1:549 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/1:550 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/1:549-550 17 atoms, 16 bonds, 2 residues, 1 model selected > select #2/1:552 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #2/1:549 16 atoms, 14 bonds, 2 residues, 1 model selected > select add #2/1:553 25 atoms, 22 bonds, 3 residues, 1 model selected > open ""/Users/enniodamico/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Desktop/All data/Stamps project/00-Paper- > FinalData/Figures/HOOK3/HOOK3-PE.cxs"" Opened postprocess_masked.mrc as #2, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 0 as #3.1, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 1 as #3.2, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 2 as #3.3, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 3 as #3.4, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 4 as #3.5, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 5 as #3.6, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 6 as #3.7, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/enniodamico/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Desktop/All data/Stamps project/00-Paper- > FinalData/Figures/HOOK3/HOOK3-PE.cxs"" Opened postprocess_masked.mrc as #2, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 0 as #3.1, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 1 as #3.2, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 2 as #3.3, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 3 as #3.4, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 4 as #3.5, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 5 as #3.6, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 6 as #3.7, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Log from Thu Mar 6 18:28:01 2025 Startup Messages --- warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle 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/enniodamico/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Desktop/All data/Stamps project/00-Paper- > FinalData/Figures/HOOK3/0120-1-HOOK23-fitted-097-coot-0.pdb"" Summary of feedback from opening /Users/enniodamico/Library/CloudStorage/OneDrive- MRCLaboratoryofMolecularBiology/Desktop/All data/Stamps project/00-Paper- FinalData/Figures/HOOK3/0120-1-HOOK23-fitted-097-coot-0.pdb --- warnings | End residue of secondary structure not found: HELIX 1 1 GLN 1 2 GLU 1 118 1 117 End residue of secondary structure not found: HELIX 2 2 GLN 2 2 GLU 2 118 1 117 Start residue of secondary structure not found: HELIX 3 3 VAL 3 2 THR 3 88 1 87 Start residue of secondary structure not found: HELIX 5 5 PRO 3 111 ARG 3 119 1 9 Start residue of secondary structure not found: HELIX 6 6 VAL 4 2 THR 4 89 1 88 Start residue of secondary structure not found: HELIX 7 7 LEU 4 104 GLU 4 107 1 4 Start residue of secondary structure not found: HELIX 8 8 PRO 4 111 ARG 4 119 1 9 Chain information for 0120-1-HOOK23-fitted-097-coot-0.pdb #1 --- Chain | Description 1 2 | No description available 3 | No description available 4 | No description available J | No description available U | No description available W | No description available Y | No description available > open ""/Users/enniodamico/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Desktop/All data/Stamps project/00-Paper- > FinalData/Figures/HOOK3/postprocess_masked.mrc"" Opened postprocess_masked.mrc as #2, grid size 300,300,300, pixel 1.3, shown at level 0.000277, step 2, values float32 > volume #2 level 0.007573 > volume #2 step 1 > select add #2 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-23.159,0,1,0,-6.0683,0,0,1,2.4677 > view matrix models #2,1,0,0,-13.392,0,1,0,-35.894,0,0,1,-1.9091 > fitmap #1 inMap #2 Fit molecule 0120-1-HOOK23-fitted-097-coot-0.pdb (#1) to map postprocess_masked.mrc (#2) using 10972 atoms average map value = 0.0107, steps = 108 shifted from previous position = 12.2 rotated from previous position = 0.614 degrees atoms outside contour = 3672, contour level = 0.0075733 Position of 0120-1-HOOK23-fitted-097-coot-0.pdb (#1) relative to postprocess_masked.mrc (#2) coordinates: Matrix rotation and translation 0.99996402 -0.00221674 -0.00818848 18.18354586 0.00227019 0.99997614 0.00652448 38.94295176 0.00817382 -0.00654283 0.99994519 12.53976943 Axis -0.61018778 -0.76404969 0.20952074 Axis point -2518.03270899 0.00000000 -616.55897014 Rotation angle (degrees) 0.61351283 Shift along axis -38.22238598 > set bgColor white > lighting soft > show atoms > hide atoms > show cartoons > dssp > cartoon style width 3.5 thickness 1.2 > volume #2 level 0.01 > volume #2 level 0.008 > color #2 #b2b2b2b3 models > color /1-2 gold > color /3-4 orange > color /W forestgreen > color /W olivedrab > color /V chartreuse > hide #!2 models > color /U chartreuse > color /Y limegreen > color /J mediumseagreen > select clear > ui tool show ""Surface Color"" > ui tool show ""Color Zone"" > show #!2 models > color zone #2 near #1 distance 7.81 [Repeated 1 time(s)] > color zone #2 near #1 distance 5 > color zone #2 near #1 distance 4 [Repeated 1 time(s)] > color single #2 > color zone #2 near #1 distance 4.8 > volume splitbyzone #2 Opened postprocess_masked.mrc 0 as #3.1, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 1 as #3.2, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 2 as #3.3, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 3 as #3.4, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 4 as #3.5, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 5 as #3.6, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 Opened postprocess_masked.mrc 6 as #3.7, grid size 300,300,300, pixel 1.3, shown at level 0.008, step 1, values float32 > hide #!3.1 models > ui tool show ""Hide Dust"" > hide #!3.2 models > hide #!3.3 models > surface dust #3.4 size 7.81 > surface dust #3.5 size 7.81 > surface dust #3.6 size 7.81 > surface dust #3.7 size 7.81 > hide ~/1-4 cartoons > select clear > save ""/Users/enniodamico/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Desktop/All data/Stamps project/00-Paper- > FinalData/Figures/HOOK3/HOOK3-PE.png"" width 1910 height 1263 supersample 3 > transparentBackground true > view name PE > graphics silhouettes width 10 > graphics silhouettes true > graphics depthjump 0.01 Expected a keyword > graphics silhouettes depthJump 0.01 > select clear [Repeated 1 time(s)] > save ""/Users/enniodamico/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Desktop/All data/Stamps project/00-Paper- > FinalData/Figures/HOOK3/HOOK3-PE.png"" width 1910 height 1263 supersample 3 > transparentBackground true > view name PE > ui tool show ""Show Sequence Viewer"" > sequence chain /1 /2 Alignment identifier is 1 > color /1-2 orange > color /3-4 gold > save ""/Users/enniodamico/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Desktop/All data/Stamps project/00-Paper- > FinalData/Figures/HOOK3/HOOK3-PE.png"" width 1910 height 1263 supersample 3 > transparentBackground true > view PER Expected an objects specifier or a view name or a keyword > view PE > save ""/Users/enniodamico/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Desktop/All data/Stamps project/00-Paper- > FinalData/Figures/HOOK3/HOOK3-PE.png"" width 1910 height 1263 supersample 3 > transparentBackground true > ui tool show ""Show Sequence Viewer"" > sequence chain /3 Alignment identifier is 1/3 > save ""/Users/enniodamico/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Desktop/All data/Stamps project/00-Paper- > FinalData/Figures/HOOK3/HOOK3-PE.cxs"" includeMaps true ——— End of log from Thu Mar 6 18:28:01 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGQ3B/A Chip: Unknown Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.101.3 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 9 days, 2 hours, 19 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 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: No 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-Clipper: 0.22.3 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-ISOLDE: 1.7 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 all ChimeraX