id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18610 PySide6: a couple of errors chimerax-bug-report@… Zach Pearson "{{{ The following bug report has been submitted: Platform: macOS-13.7.4-x86_64-i386-64bit ChimeraX Version: 1.11.dev202508140657 (2025-08-14 06:57:21 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000700016575000 (most recent call first): File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000700015572000 (most recent call first): File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000070001456f000 (most recent call first): File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 948 in wait File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", 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""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000700012569000 (most recent call first): File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000700011566000 (most recent call first): File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000700010563000 (most recent call first): File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Current thread 0x00007ff8455a39c0 (most recent call first): File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1058 in init File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1223 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, shiboken6.Shiboken, PySide6.QtCore, PySide6.QtGui, PySide6.QtWidgets, PySide6.QtNetwork, PySide6.QtPrintSupport, PySide6.QtWebChannel, PySide6.QtWebEngineCore, 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2.7G 3058 \nTOTAL, minus reserved VM space 2.3G 3058 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""6ba5b6c2007c27a443a90646cb1c4412cc6f5193"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62c751b6bcb0435c2153fe92"", ""factorPackIds"" : { ""SIRI_UNDERSTANDING_ASR_ASSISTANT"" : ""6317ae3a3d24842ff84fd83f"", ""SIRI_UNDERSTANDING_MORPHUN"" : ""64e514ddc83b9a3d50649ddc"" }, ""deploymentId"" : 240000366 }, { ""rolloutId"" : ""63582c5f8a53461413999550"", ""factorPackIds"" : { }, ""deploymentId"" : 240000002 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.dev202508140657 (2025-08-14) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/navya/Downloads/fold_cytochrome_p450_3a4_isoform_1_homo_sapiens/fold_cytochrome_p450_3a4_isoform_1_homo_sapiens_full_data_0.json Opening an AlphaFold PAE file requires first opening the predicted atomic model. Did not find an open atomic model from the same directory. If the atomic model is already open choose it using menu Tools / Structure Prediction / AlphaFold Error Plot or use the open command structure option, for example open /Users/navya/Downloads/fold_cytochrome_p450_3a4_isoform_1_homo_sapiens/fold_cytochrome_p450_3a4_isoform_1_homo_sapiens_full_data_0.json structure #1 If you are trying to open a JSON file that is not AlphaFold PAE data then you need to specify the specific JSON format such as open mole_channels.json format mole > open ""/Users/navya/Downloads/fold_cytochrome_p450_3a4_isoform_1_homo_sapiens > (1)/fold_cytochrome_p450_3a4_isoform_1_homo_sapiens_model_4.cif"" Chain information for fold_cytochrome_p450_3a4_isoform_1_homo_sapiens_model_4.cif #1 --- Chain | Description A | . Computing secondary structure > color bfactor pal alpha 4034 atoms, 503 residues, atom bfactor range 21.3 to 99 > ui tool show ""Render/Select by Attribute"" Traceback (most recent call last): File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 1400, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/render_by_attr/__init__.py"", line 39, in start_tool return RenderByAttrTool(session, tool_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/render_by_attr/tool.py"", line 339, in __init__ self._update_target_menu() File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/render_by_attr/tool.py"", line 940, in _update_target_menu menu.clear() ^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'clear' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py"", line 1891, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3230, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/cmd.py"", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Render/Select by Attribute in bundle ChimeraX-RenderByAttr: 'NoneType' object has no attribute 'clear' chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Render/Select by Attribute in bundle ChimeraX-RenderByAttr: 'NoneType' object has no attribute 'clear' File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. > save plddt_values.csv format csv Unknown data format: 'csv' > ui tool show ""Render/Select by Attribute"" Traceback (most recent call last): File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/render_by_attr/tool.py"", line 757, in _update_select_attr_menu attr_names = self._attr_names_of_type(int, float, bool, str) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/render_by_attr/tool.py"", line 543, in _attr_names_of_type attr_info = self._cur_attr_info() ^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/render_by_attr/tool.py"", line 584, in _cur_attr_info return self._ui_to_info[target] ~~~~~~~~~~~~~~~~^^^^^^^^ KeyError: '' KeyError: '' File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/render_by_attr/tool.py"", line 584, in _cur_attr_info return self._ui_to_info[target] ~~~~~~~~~~~~~~~~^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/render_by_attr/tool.py"", line 757, in _update_select_attr_menu attr_names = self._attr_names_of_type(int, float, bool, str) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/render_by_attr/tool.py"", line 543, in _attr_names_of_type attr_info = self._cur_attr_info() ^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/render_by_attr/tool.py"", line 584, in _cur_attr_info return self._ui_to_info[target] ~~~~~~~~~~~~~~~~^^^^^^^^ KeyError: '' KeyError: '' File ""/Applications/ChimeraX_Techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/render_by_attr/tool.py"", line 584, in _cur_attr_info return self._ui_to_info[target] ~~~~~~~~~~~~~~~~^^^^^^^^ See log for complete Python traceback. ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.dev202508140657 (2025-08-14) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-20.7.3 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640 OpenGL vendor: Intel Inc. Python: 3.11.9 Locale: UTF-8 Qt version: PySide6 6.9.1, Qt 6.9.1 Qt runtime version: 6.9.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 529.140.2.0.0 OS Loader Version: 577.140.2~30 SMC Version (system): 2.43f11 Software: System Software Overview: System Version: macOS 13.7.4 (22H420) Kernel Version: Darwin 22.6.0 Time since boot: 2 days, 18 hours, 2 minutes Graphics/Displays: Intel Iris Plus Graphics 640: Chipset Model: Intel Iris Plus Graphics 640 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5926 Revision ID: 0x0006 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.4 blockdiag: 3.0.0 blosc2: 3.7.0 build: 1.2.2.post1 certifi: 2025.7.14 cftime: 1.6.4.post1 charset-normalizer: 3.4.3 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.0.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.12 ChimeraX-AtomicLibrary: 14.1.22 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.dev202508140657 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: 1.7.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 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-MDcrds: 2.17 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.5.1 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: 1.15.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 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: 1.1.3 ChimeraX-ProfileGrids: 1.1.4 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.4 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: 1.5.2 ChimeraX-Scenes: 0.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.2 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: 1.48.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.3 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: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.10.3 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.2 debugpy: 1.8.16 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.1 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.30.1 ipython: 9.4.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.7 jedi: 0.19.2 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 5.3.1 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PySide6: 6.9.1 PySide6_Addons: 6.9.1 PySide6_Essentials: 6.9.1 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.1 qtconsole: 5.6.1 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 requests: 2.32.4 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 shiboken6: 6.9.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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 stack-data: 0.6.3 superqt: 0.7.5 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.2 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Window Toolkit fixed chimera-programmers all ChimeraX