id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20471 Crash in NSAccessibility routines chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.0-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/berivanaksoy/Desktop/final structure.pdb"" format pdb Summary of feedback from opening /Users/berivanaksoy/Desktop/final structure.pdb --- warnings | End residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20 0 Start residue of secondary structure not found: HELIX 1 1 ARG A 57 LEU A 69 1 13 Start residue of secondary structure not found: HELIX 2 2 LEU A 98 ASP A 104 1 7 Start residue of secondary structure not found: HELIX 3 3 THR A 110 HIS A 131 1 22 Start residue of secondary structure not found: HELIX 4 4 LYS A 139 ASN A 141 1 3 Start residue of secondary structure not found: HELIX 5 5 VAL A 174 ARG A 179 1 6 8 messages similar to the above omitted End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307 1 5 Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20 0 Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30 0 Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42 0 Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80 0 Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92 0 16 messages similar to the above omitted End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307 1 5 Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20 0 Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30 0 Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42 0 Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80 0 Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92 0 16 messages similar to the above omitted End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307 1 5 Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20 0 Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30 0 Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42 0 Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80 0 Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92 0 16 messages similar to the above omitted End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307 1 5 Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20 0 Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30 0 Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42 0 Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80 0 Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92 0 16 messages similar to the above omitted End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307 1 5 Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20 0 Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30 0 Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42 0 Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80 0 Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92 0 16 messages similar to the above omitted End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307 1 5 Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20 0 Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30 0 Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42 0 Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80 0 Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92 0 16 messages similar to the above omitted End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307 1 5 Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20 0 Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30 0 Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42 0 Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80 0 Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92 0 16 messages similar to the above omitted End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307 1 5 Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20 0 Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30 0 Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42 0 Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80 0 Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92 0 16 messages similar to the above omitted End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307 1 5 Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20 0 Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30 0 Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42 0 Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80 0 Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92 0 16 messages similar to the above omitted End residue of secondary structure not found: HELIX 14 14 PRO A 303 LEU A 307 1 5 Start residue of secondary structure not found: SHEET 1 1 1 GLU A 13 GLU A 20 0 Start residue of secondary structure not found: SHEET 2 2 1 THR A 25 ARG A 30 0 Start residue of secondary structure not found: SHEET 3 3 1 ILE A 37 LYS A 42 0 Start residue of secondary structure not found: SHEET 4 4 1 LEU A 77 ALA A 80 0 Start residue of secondary structure not found: SHEET 5 5 1 SER A 88 ASP A 92 0 25 messages similar to the above omitted 7 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 2176 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. 44 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 2273 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. 30 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 2260 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. 44 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 2273 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. Chain information for final structure.pdb --- Chain | Description 1.1/A | No description available 1.2/A 1.9/A | No description available 1.3/A | No description available 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A | No description available 1.15/A | No description available Computing secondary structure > hide #!1.1 models > hide #!1.2 models > hide #!1.3 models > hide #1.4 models > hide #1.5 models > hide #1.6 models > hide #1.7 models > hide #!1.9 models > hide #1.8 models > hide #1.10 models > hide #1.11 models > hide #1.12 models > hide #1.13 models > hide #1.14 models > hide #1.15 models > log metadata No models had metadata > show #1.15 models > log metadata No models had metadata > info attributes models #1.* Expected a models specifier or a keyword > hide #1.15 models > show #1.14 models > hide #1.14 models > show #1.13 models > hide #1.13 models > show #1.12 models > hide #1.12 models > show #1.11 models > hide #1.11 models > show #1.10 models > hide #1.10 models > show #!1.9 models > hide #!1.9 models > view #1.3 clip false > close > open CT7030 'CT7030' has no suffix > open 8p4z 8p4z title: Crystal structure of the human CDK7 kinase domain in complex with LDC4297 [more info...] Chain information for 8p4z #1 --- Chain | Description | UniProt A B | Cyclin-dependent kinase 7 | CDK7_HUMAN 10-311 Non-standard residues in 8p4z #1 --- 1PE — pentaethylene glycol (PEG400) GOL — glycerol (glycerin; propane-1,2,3-triol) PGE — triethylene glycol WZ8 — 2-[(3R)-piperidin-3-yl]oxy-8-propan-2-yl-N-[(2-pyrazol-1-ylphenyl)methyl]pyrazolo[1,5-a][1,3,5]triazin-4-amine 8p4z mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 22 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 4531 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > open 8r99 8r99 title: A soakable crystal form of human CDK7 in complex with AMP-PNP [more info...] Chain information for 8r99 #2 --- Chain | Description | UniProt A | Cyclin-dependent kinase 7 | CDK7_HUMAN 1-346 Non-standard residues in 8r99 #2 --- ANP — phosphoaminophosphonic acid-adenylate ester MG — magnesium ion 30 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 2260 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > open 8r9a Summary of feedback from opening 8r9a fetched from pdb --- warning | Atom H32 is not in the residue template for I74 /A:402 8r9a title: A soakable crystal form of human CDK7 in complex with AMP-PNP [more info...] Chain information for 8r9a #3 --- Chain | Description | UniProt A | Cyclin-dependent kinase 7 | CDK7_HUMAN 1-346 Non-standard residues in 8r9a #3 --- I74 — (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl- pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol PEG — di(hydroxyethyl)ether 44 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 2273 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > hide atoms > delete #3/B > delete ~/A > delete solvent > matchmaker #1 to #3 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 8r9a, chain A (#3) with 8p4z, chain A (#1), sequence alignment score = 1463.7 RMSD between 249 pruned atom pairs is 0.532 angstroms; (across all 269 pairs: 1.793) > open > ./Gene433_FinalReport_Documents_Berivan_Aksoy/Sequences/cdk20_isoform3_Homosapiens.fasta Summary of feedback from opening ./Gene433_FinalReport_Documents_Berivan_Aksoy/Sequences/cdk20_isoform3_Homosapiens.fasta --- note | Alignment identifier is cdk20_isoform3_Homosapiens.fasta Opened 1 sequence from cdk20_isoform3_Homosapiens.fasta > sequence associate #1/A,2/A,3/A cdk20_isoform3_Homosapiens.fasta:1 Associated 8p4z chain A to NP_001034892.1 cyclin-dependent kinase 20 isoform 3 [Homo sapiens] with 173 mismatches and/or gaps ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 86 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.9 Locale: UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir10,1 Model Number: MGN63TU/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 163 days, 1 hour, 17 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 7 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 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: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 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: 1.19.1 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: 2.5.2 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: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 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 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Window Toolkit duplicate all ChimeraX