id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16468 Crash in garbage collection chhandosee@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-arm64-arm-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 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 0x00000001fdeffac0 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_weakrefset.py"", line 58 in _commit_removals File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_weakrefset.py"", line 33 in __exit__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_weakrefset.py"", line 64 in __iter__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/nucleotides/_data.py"", line 519 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/nucleotides/_data.py"", line 519 in rebuild File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 65 in draw_new_frame File 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/State4b_J92.pdb"" Chain information for State4b_J92.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > open ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/State4a_98.pdb"" Chain information for State4a_98.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > hide #!1 models > close session > open ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/Maps/J98 z flip.mrc"" Opened J98 z flip.mrc as #1, grid size 280,280,280, pixel 0.86, shown at level 0.0408, step 2, values float32 > surface dust #1 size 8.6 > open ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/State4a_98-121324_real_space_refined_027.pdb"" Chain information for State4a_98-121324_real_space_refined_027.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > volume #1 level 0.03299 > transparency 50 > set bgColor white > set bgColor #ffffff00 > lighting soft > open > /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J98_008_volume_map_half_A.mrc Opened J98_008_volume_map_half_A.mrc as #3, grid size 280,280,280, pixel 0.86, shown at level 0.322, step 2, values float32 > open > /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J98_008_volume_map_half_B.mrc Opened J98_008_volume_map_half_B.mrc as #4, grid size 280,280,280, pixel 0.86, shown at level 0.323, step 2, values float32 > volume flip #3 Opened J98_008_volume_map_half_A.mrc z flip as #5, grid size 280,280,280, pixel 0.86, shown at step 1, values float32 > volume flip #4 Opened J98_008_volume_map_half_B.mrc z flip as #6, grid size 280,280,280, pixel 0.86, shown at step 1, values float32 > volume #5 level 0.1226 > volume #5 level 0.3097 > save ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/Maps/98_half_map_A_zflipped.mrc"" models #5 > save ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/Maps/98_half_map_B_zflipped.mrc"" models #6 > volume #5 level 0.4848 > volume #5 level 0.3335 > hide #!1 models > volume #5 level 0.242 > surface dust #5 size 8.6 > volume #5 level 0.1306 > volume #5 level 0.16 > volume #5 level 0.17 > volume #5 level 0.18 > volume #5 level 0.16 > surface dust #6 size 8.6 > volume #6 level 0.16 > hide #!6 models > show #!1 models > hide #!2 models > volume #!1 style surface > color #1 #797979ff models > volume #!1 step 1 > volume #1 level 0.03581 > save ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/Maps/S4a_J98.tif"" width 893 height 939 supersample 3 > transparentBackground true > save ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/Maps/S4a_98.png"" width 893 height 939 supersample 3 > transparentBackground true > show #!2 models > hide #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 2/B > select /B:-19 22 atoms, 24 bonds, 1 residue, 1 model selected > select /B 764 atoms, 854 bonds, 36 residues, 1 model selected > open ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/State4a_98-121324_real_space_refined_027.pdb"" Chain information for State4a_98-121324_real_space_refined_027.pdb #7 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > open > /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J94_008_volume_map_half_A.mrc > /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J94_008_volume_map_half_B.mrc Opened J94_008_volume_map_half_A.mrc as #8.1, grid size 280,280,280, pixel 0.86, shown at level 0.311, step 2, values float32 Opened J94_008_volume_map_half_B.mrc as #8.2, grid size 280,280,280, pixel 0.86, shown at level 0.312, step 2, values float32 > hide #!7 models > hide #!8 models > close session > open > /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J94_008_volume_map_half_A.mrc Opened J94_008_volume_map_half_A.mrc as #1, grid size 280,280,280, pixel 0.86, shown at level 0.311, step 2, values float32 > open > /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J94_008_volume_map_half_B.mrc Opened J94_008_volume_map_half_B.mrc as #2, grid size 280,280,280, pixel 0.86, shown at level 0.312, step 2, values float32 > open ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/Maps/J94 z flip.mrc"" Opened J94 z flip.mrc as #3, grid size 280,280,280, pixel 0.86, shown at level 0.059, step 2, values float32 > volume flip #1 Opened J94_008_volume_map_half_A.mrc z flip as #4, grid size 280,280,280, pixel 0.86, shown at step 1, values float32 > volume flip #2 Opened J94_008_volume_map_half_B.mrc z flip as #5, grid size 280,280,280, pixel 0.86, shown at step 1, values float32 > open ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/State3_94 121324_real_space_refined_030.pdb"" Chain information for State3_94 121324_real_space_refined_030.pdb #6 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > surface dust #3 size 8.6 > surface dust #4 size 8.6 > surface dust #5 size 8.6 > transparency #3.1#4.1#5.1 50 > volume #3 level 0.082 > volume #!3-5 style surface > color #3 #797979ff models > volume #3 level 0.07048 > volume #!3-5 step 1 > volume #3 level 0.06516 > hide #!3 models > hide #!5 models > volume #4 level 0.2766 > volume #4 level 0.2268 > volume #4 level 0.1847 > volume #4 level 0.1426 > surface dust #4 size 8.6 > volume #4 level 0.177 > save ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/Maps/94_half_map_A_zflipped.mrc"" models #4 > save ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/Maps/94_half_map_B_zflipped.mrc"" models #5 > volume #5 level 0.177 > hide #!3 models > show #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > save ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/Maps/S3_94.png"" width 597 height 939 supersample 3 > transparentBackground true > close session > open ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/J96_State2/J96 z flip.mrc"" Opened J96 z flip.mrc as #1, grid size 280,280,280, pixel 0.86, shown at level 0.0288, step 2, values float32 > open ""/Users/chhandoseeganguly/Desktop/Cas12a_models/cas12a_MCH_final/Final > Structures/J96_State2/State2_96_121324_real_space_refined_029.pdb"" Chain information for State2_96_121324_real_space_refined_029.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J96_008_volume_map_half_A.mrc Opened J96_008_volume_map_half_A.mrc as #3, grid size 280,280,280, pixel 0.86, shown at level 0.311, step 2, values float32 > open > /Users/chhandoseeganguly/Desktop/Cas12a_models/Half_maps/J96_008_volume_map_half_B.mrc Opened J96_008_volume_map_half_B.mrc as #4, grid size 280,280,280, pixel 0.86, shown at level 0.311, step 2, values float32 > surface dust #1 size 8.6 > surface dust #3 size 8.6 > surface dust #4 size 8.6 > volume flip #3 Opened J96_008_volume_map_half_A.mrc z flip as #5, grid size 280,280,280, pixel 0.86, shown at step 1, values float32 > volume flip #4 Opened J96_008_volume_map_half_B.mrc z flip as #6, grid size 280,280,280, pixel 0.86, shown at step 1, values float32 > volume #3 level 0.16 > close #3 > close #4 > volume #5 level 0.177 > volume #5 level 0.2 > volume #5 level 0.3 > hide #!1 models > hide #!6 models ===== Log before crash end ===== Log: 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: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 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: iMac Model Identifier: iMac21,1 Model Number: Z12Q000NULL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 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: 4 days, 7 hours, 21 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 4.5K (4480 x 2520) 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: 0.1.3 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: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 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: 0.22.4 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: 1.7.1 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: 1.7.1 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: 2.6.1 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: 1.5.14 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: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.2.2 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-QScore: 1.1 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: 1.12.4 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: 1.33.3 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: 0.2.1 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: 4.47.2 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: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 MolecularDynamicsViewer: 1.4 msgpack: 1.0.4 nest-asyncio: 1.6.0 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: 10.2.0 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: 1.0.8 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: 0.5.0 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: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate all ChimeraX