id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16854 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.9rc202411012347 (2024-11-01 23:47:45 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/sb2364/Downloads/fold_cseda01_deaminase_only/fold_cseda01_deaminase_only_model_4.cif Chain information for fold_cseda01_deaminase_only_model_4.cif #1 --- Chain | Description A | . Computing secondary structure > open > /Users/sb2364/Downloads/fold_cseda01_mci8316215_imm1/fold_cseda01_mci8316215_imm1_model_4.cif Chain information for fold_cseda01_mci8316215_imm1_model_4.cif #2 --- Chain | Description A | . B | . Computing secondary structure > ui tool show Matchmaker > matchmaker #2 to #1 Computing secondary structure 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 fold_cseda01_deaminase_only_model_4.cif, chain A (#1) with fold_cseda01_mci8316215_imm1_model_4.cif, chain A (#2), sequence alignment score = 886.4 RMSD between 163 pruned atom pairs is 0.583 angstroms; (across all 178 pairs: 2.417) > ui dockable false ""Model Panel"" > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > ui tool show Log > select add #1 1395 atoms, 1416 bonds, 178 residues, 1 model selected > select subtract #1 Nothing selected > select add #2 2676 atoms, 2728 bonds, 338 residues, 1 model selected > select subtract #2 Nothing selected > select add #2 2676 atoms, 2728 bonds, 338 residues, 1 model selected > hide #2 models > show #2 models > hide #1 models > delete 2/A Missing or invalid ""atoms"" argument: invalid atoms specifier > delete 2/a Missing or invalid ""atoms"" argument: invalid atoms specifier > delete /a > open > /Users/sb2364/Downloads/fold_cseda01_deaminase_only/fold_cseda01_deaminase_only_model_4.cif Chain information for fold_cseda01_deaminase_only_model_4.cif #1 --- Chain | Description A | . Computing secondary structure > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_cseda01_mci8316215_imm1_model_4.cif_B SES surface #2.1: minimum, -23.11, mean -7.33, maximum 6.64 To also show corresponding color key, enter the above coulombic command and add key true > select subtract #2 1 model selected > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_cseda01_mci8316215_imm1_model_4.cif_B SES surface #2.1: minimum, -23.11, mean -7.33, maximum 6.64 Coulombic values for fold_cseda01_deaminase_only_model_4.cif_A SES surface #1.1: minimum, -16.11, mean 0.09, maximum 20.59 To also show corresponding color key, enter the above coulombic command and add key true > coulombic Coulombic values for fold_cseda01_mci8316215_imm1_model_4.cif_B SES surface #2.1: minimum, -23.11, mean -7.33, maximum 6.64 Coulombic values for fold_cseda01_deaminase_only_model_4.cif_A SES surface #1.1: minimum, -16.11, mean 0.09, maximum 20.59 To also show corresponding color key, enter the above coulombic command and add key true > hide surfaces > show surfaces > hide surfaces > transparency 40 > coulombic Coulombic values for fold_cseda01_mci8316215_imm1_model_4.cif_B SES surface #2.1: minimum, -23.11, mean -7.33, maximum 6.64 Coulombic values for fold_cseda01_deaminase_only_model_4.cif_A SES surface #1.1: minimum, -16.11, mean 0.09, maximum 20.59 To also show corresponding color key, enter the above coulombic command and add key true > transparency 30 > transparency 80 > combine > hide #!2 models > hide #!1 models > hide #3 models > show #3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > mlp #3 Map values for surface ""combination_A SES surface"": minimum -29.3, mean -5.584, maximum 22 Map values for surface ""combination_B SES surface"": minimum -27.58, mean -5.263, maximum 22.24 To also show corresponding color key, enter the above mlp command and add key true > transparency #3 80 > hide #3.2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!1 models > hide #!3 models > show #!2 models > hide #2.1 models > hide #!1-2 cartoons > hide #!2 models > show #!2 models > show #2.1 models > hide #1.1 models > hide #2.1 models > show #1.1 models > show #2.1 models > hide #1.1 models > hide #2.1 models > show #1.1 models > show #2.1 models > transparency #1-2 80 > transparency #1-2 70 > transparency #1-2 90 > hide #!1-2 cartoons > show #!1-2 cartoons > transparency #1-2 50 > hide #1.1 models > show #1.1 models > hide #2.1 models > hide #3.1 models > show #3.1 models > hide #3.1 models > show #2.1 models > hide #1.1 models > findclash Unknown command: findclash > ~findclash Unknown command: ~findclash > ~findclash Unknown command: ~findclash > interfaces ~solvent 6 buried areas: #1/A #3/A 7759, #3/B #2/B 4427, #1/A #3/B 1527, #1/A #2/B 1527, #3/A #2/B 1527, #3/A #3/B 1527 > ~hbonds > hbonds reveal true 1247 hydrogen bonds found > ~hbonds > hbonds reveal true 1247 hydrogen bonds found > ~hbonds > hbonds reveal true 1247 hydrogen bonds found > hbonds reveal true 1247 hydrogen bonds found > style stick Changed 5352 atom styles > style sphere Changed 5352 atom styles > style ball Changed 5352 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides fill > style nucleic stick Changed 0 atom styles > hide atoms > ~distance all > ui windowfill toggle > ~distance all > ui tool show Log > ~distance all > ui tool show ""Side View"" > ui tool show ""Volume Viewer"" > ui tool show ViewDockX No suitable models found for ViewDockX > ui tool show Clashes > clashes ignoreHiddenModels true color #0cdc07 15622 clashes > ui tool show ""Model Panel"" > hide #4 models > hide #!3 models > hide #2.1 models > hide #!2 models > hide #!1 models > show #!3 models > show #4 models > hide #4 models > hide #5 models > show #5 models > show #!1 models > close #5 > close #3.1 > close #3.2 > hide #3 models > show #3 models > hide #!1 models > show #!1 models > ui tool show Clashes > clashes overlapCutoff 1.3 ignoreHiddenModels true color #0cdc07 4379 clashes > hide #5 models > show #5 models > show #4 models > hide #4 models > hide #5 models > show #5 models > hide #5 models > close #5 > ui tool show Clashes > clashes ignoreHiddenModels true color #15dc18 radius 0.21 8058 clashes > show #2.1 models > ui tool show ""Find Cavities"" > kvfinder #1,3 10 cavities found for fold_cseda01_deaminase_only_model_4.cif #1 fold_cseda01_deaminase_only_model_4.cif Cavities --- ID | | Volume | Area | Points 1.2.4 | | 109.08 | 114.5 | 505 1.2.6 | | 45.36 | 64.37 | 210 1.2.8 | | 44.06 | 61.64 | 204 1.2.2 | | 34.34 | 50.72 | 159 1.2.3 | | 25.7 | 36.48 | 119 1.2.1 | | 22.46 | 32.23 | 104 1.2.9 | | 22.03 | 39.42 | 102 1.2.5 | | 12.31 | 29.54 | 57 1.2.7 | | 10.58 | 18.96 | 49 1.2.10 | | 6.26 | 15.59 | 29 14 cavities found for combination #3 combination Cavities --- ID | | Volume | Area | Points 3.1.11 | | 500.9 | 382.98 | 2319 3.1.4 | | 290.52 | 262.41 | 1345 3.1.5 | | 264.6 | 222.43 | 1225 3.1.1 | | 228.53 | 232.81 | 1058 3.1.10 | | 73.66 | 88.2 | 341 3.1.12 | | 43.2 | 57.66 | 200 3.1.8 | | 26.14 | 46.24 | 121 3.1.3 | | 21.38 | 33.27 | 99 3.1.9 | | 19.87 | 36.19 | 92 3.1.14 | | 19.01 | 31.31 | 88 3.1.7 | | 17.28 | 36.68 | 80 3.1.6 | | 7.34 | 13.91 | 34 3.1.2 | | 6.91 | 14.38 | 32 3.1.13 | | 5.62 | 13.39 | 26 > show #1.1 models > hide #1.1 models > hide #2.1 models > show #2.1 models > hide #2.1 models > ui tool show Foldseek > foldseek #!3/B Found 20 similar structures to combination #!3/B in pdb database using foldseek, name fs1 > open 6anz Summary of feedback from opening 6anz fetched from pdb --- notes | Fetching compressed mmCIF 6anz from http://files.rcsb.org/download/6anz.cif Fetching CCD SO4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif 6anz title: Crystal structure of a hypothetical protein from Neisseria gonorrhoeae [more info...] Chain information for 6anz #6 --- Chain | Description | UniProt A | Uncharacterized protein | B4RQJ2_NEIG2 1-138 Non-standard residues in 6anz #6 --- SO4 — sulfate ion 6anz mmCIF Assemblies --- 1| software_defined_assembly 61 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 5 C-terminal residues, 37 non-polymer residues more than 3.0 Angstroms away. Alignment of 6anz chain A to query has RMSD 1.18 using 47 of 124 paired residues within cutoff distance 2.0 > open 6anz 6anz title: Crystal structure of a hypothetical protein from Neisseria gonorrhoeae [more info...] Chain information for 6anz #7 --- Chain | Description | UniProt A | Uncharacterized protein | B4RQJ2_NEIG2 1-138 Non-standard residues in 6anz #7 --- SO4 — sulfate ion 6anz mmCIF Assemblies --- 1| software_defined_assembly 61 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 5 C-terminal residues, 37 non-polymer residues more than 3.0 Angstroms away. Alignment of 6anz chain A to query has RMSD 1.18 using 47 of 124 paired residues within cutoff distance 2.0 > hide #7 models > hide #6 models > show #7 models > close #7 > close #6 > hide #!3.1 models > hide #!1.2 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9rc202411012347 (2024-11-01) © 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 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,6 Model Number: MRX33LL/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 11881.1.1 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 29 days, 20 hours, 33 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 HP Z24n G2: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported HP Z24i G2: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.7.1 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 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: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.7 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.7 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 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: 2.3 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: 1.9rc202411012347 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.5 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2 ChimeraX-Label: 1.1.11 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 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-MutationScores: 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: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 3.2.4 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 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: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.3.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.7 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.54.1 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.12.1 html2text: 2024.2.26 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.1 numpy: 2.1.3 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: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 plotly: 5.24.1 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pyKVFinder: 0.7.1 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.1 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tenacity: 9.0.0 tifffile: 2024.7.24 tinyarray: 1.2.4 toml: 0.10.2 tornado: 6.4.1 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX