id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15695 Close volume log equivalent command: v.session is None chimerax-bug-report@… Zach Pearson "{{{ The following bug report has been submitted: Platform: macOS-14.5-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/zhanj2/Downloads/cryosparc_P6_J847_007_volume_map.mrc Opened cryosparc_P6_J847_007_volume_map.mrc as #1, grid size 384,384,384, pixel 0.83, shown at level 0.0338, step 2, values float32 > ui tool show ""Segment Map"" Segmenting cryosparc_P6_J847_007_volume_map.mrc, density threshold 0.033819 Only showing 60 of 115 regions. Showing 60 of 115 region surfaces 1993 watershed regions, grouped to 115 regions Showing cryosparc_P6_J847_007_volume_map.seg - 115 regions, 60 surfaces Select one or more regions to delete > ui mousemode right select > select #2.24 1 model selected Deleted 1 regions > select #2.4 1 model selected Deleted 1 regions > hide #!1 models > select #2.1 1 model selected Deleted 1 regions > select #2.6 1 model selected Deleted 1 regions Ungrouped to 108 regions, but did not show all surfaces, see Options > close #2 > show #!1 models > open > /Users/zhanj2/P-gp/Krios_2023-03-13_drugs/Tariquidar/tariquidar_final_maps/20230615_Tariquidar_J484_3p16A_medium_1Tarquidar/J484_2AGS-1Tar-094_new-4DI.pdb Summary of feedback from opening /Users/zhanj2/P-gp/Krios_2023-03-13_drugs/Tariquidar/tariquidar_final_maps/20230615_Tariquidar_J484_3p16A_medium_1Tarquidar/J484_2AGS-1Tar-094_new-4DI.pdb --- warnings | Duplicate atom serial number found: 12733 Duplicate atom serial number found: 12734 Duplicate atom serial number found: 12735 Duplicate atom serial number found: 12736 Duplicate atom serial number found: 12737 23 messages similar to the above omitted Chain information for J484_2AGS-1Tar-094_new-4DI.pdb #2 --- Chain | Description A | No description available > fitmap #2 inMap #1 Fit molecule J484_2AGS-1Tar-094_new-4DI.pdb (#2) to map cryosparc_P6_J847_007_volume_map.mrc (#1) using 9275 atoms average map value = 0.1572, steps = 208 shifted from previous position = 16.8 rotated from previous position = 0.779 degrees atoms outside contour = 169, contour level = 0.033819 Position of J484_2AGS-1Tar-094_new-4DI.pdb (#2) relative to cryosparc_P6_J847_007_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.99993513 -0.00961839 0.00610042 10.68058562 0.00966342 0.99992596 -0.00739524 7.88470908 -0.00602884 0.00745371 0.99995405 10.34707498 Axis 0.54608006 0.44606177 0.70910187 Axis point -44.42907270 163.35573394 0.00000000 Rotation angle (degrees) 0.77901397 Shift along axis 16.68665236 > volume #1 step 1 > color #1 #b2b2b279 models > volume #1 level 0.06865 > ui tool show ""Color Zone"" > color zone #1 near #2 distance 4.98 > color #2 #ece39bff > color zone #1 near #2 distance 4.98 [Repeated 1 time(s)] > color zone #1 near #2 distance 5 [Repeated 2 time(s)] > color zone #1 near #2 distance 4 [Repeated 2 time(s)] > color zone #1 near #2 distance 5 [Repeated 1 time(s)] > volume splitbyzone #1 Opened cryosparc_P6_J847_007_volume_map.mrc 0 as #3.1, grid size 384,384,384, pixel 0.83, shown at level 0.0686, step 1, values float32 Opened cryosparc_P6_J847_007_volume_map.mrc 1 as #3.2, grid size 384,384,384, pixel 0.83, shown at level 0.0686, step 1, values float32 > close #3 > color zone #1 near #2 distance 5.5 > show #!1 models > color zone #1 near #2 distance 5.5 [Repeated 1 time(s)] > color zone #1 near #2 distance 5 [Repeated 1 time(s)] > hide #!1 models > show #!1 models > volume #1 level 0.0798 > volume #1 level 0.05749 > color #1 #c5c5c579 models > color #1 #c5c5c578 models > ui tool show Segmentations > ui view fourup > segmentations mouseModes false Mouse bindings not saved; ignoring 'mouseModes false' > ui view fourup > segmentations mouseModes false Mouse bindings not saved; ignoring 'mouseModes false' > close # Expected a models specifier or a keyword close # ......^ Expected a models specifier or a keyword Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/logging.py"", line 40, in log_equivalent_command command.run(command_text, log_only=True) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3175, in run raise UserError(self._error) chimerax.core.errors.UserError: Expected a models specifier or a keyword During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2138, in close_map_cb log_equivalent_command(v.session, 'close #%s' % v.id_string) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/logging.py"", line 42, in log_equivalent_command session.logger.info(str(err)) ^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'logger' AttributeError: 'NoneType' object has no attribute 'logger' File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/logging.py"", line 42, in log_equivalent_command session.logger.info(str(err)) ^^^^^^^^^^^^^^ See log for complete Python traceback. > close # Expected a models specifier or a keyword close # ......^ Expected a models specifier or a keyword Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/logging.py"", line 40, in log_equivalent_command command.run(command_text, log_only=True) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3175, in run raise UserError(self._error) chimerax.core.errors.UserError: Expected a models specifier or a keyword During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2138, in close_map_cb log_equivalent_command(v.session, 'close #%s' % v.id_string) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/logging.py"", line 42, in log_equivalent_command session.logger.info(str(err)) ^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'logger' AttributeError: 'NoneType' object has no attribute 'logger' File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/logging.py"", line 42, in log_equivalent_command session.logger.info(str(err)) ^^^^^^^^^^^^^^ See log for complete Python traceback. close # ......^ Expected a models specifier or a keyword Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/logging.py"", line 40, in log_equivalent_command command.run(command_text, log_only=True) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3175, in run raise UserError(self._error) chimerax.core.errors.UserError: Expected a models specifier or a keyword During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2138, in close_map_cb log_equivalent_command(v.session, 'close #%s' % v.id_string) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/logging.py"", line 42, in log_equivalent_command session.logger.info(str(err)) ^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'logger' AttributeError: 'NoneType' object has no attribute 'logger' File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/logging.py"", line 42, in log_equivalent_command session.logger.info(str(err)) ^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2227, in select_data_cb d.display_volume_info(v) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 234, in display_volume_info p.update_panel_widgets(volume) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 1625, in update_panel_widgets hp.update_threshold_gui(message_cb = None) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2650, in update_threshold_gui self.update_shown_icon() File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/map/volume_viewer.py"", line 2341, in update_shown_icon shown = v.display ^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 389, in get_display return self._any_displayed_positions and len(self._positions) > 0 ^^^^^^^^^^^^^^^^^^^^ TypeError: object of type 'NoneType' has no len() TypeError: object of type 'NoneType' has no len() File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 389, in get_display return self._any_displayed_positions and len(self._positions) > 0 ^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,2 Model Number: Z14W0010DLL/A Chip: Unknown Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 64 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 6 hours, 48 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL U2723QE: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes DELL U2718Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 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: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 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: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Volume Data fixed Tom Goddard all ChimeraX