id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19021 Didn't find section 'Peptide bond' in tab 'ISOLDE' chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-5.14.0-427.22.1.el9_4.x86_64-x86_64-with-glibc2.34 ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC) Description happens when you click on a qscore residue in the chimerx window Log: UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /home/walter/refine/CEM-1332D4-KP311/S-closed-1332D4/J518_005_volume_map.mrc Opened J518_005_volume_map.mrc as #1, grid size 512,512,512, pixel 0.73, shown at level 0.0147, step 2, values float32 > volume #1 level 0.04289 > open > /home/walter/refine/CEM-1332D4-KP311/S-closed-1332D4/RealSpaceRefine_18/trimer-717-v1-remove- > header_real_space_refined_018.pdb Chain information for trimer-717-v1-remove-header_real_space_refined_018.pdb #2 --- Chain | Description A E | No description available B | No description available > toolshed show Downloading bundle ChimeraX_QScore-1.2-cp311-cp311-linux_x86_64.whl Installed ChimeraX-QScore (1.2) > qscore #2 toVolume #1 When the ""qscore"" command is called with ""useGui True"", the analysis will be run on the entire model. > ui tool show ""Model-map Q-Score"" > style #2 stick Changed 24700 atom styles > color #2 byhetero > transparency #1 60 Overall mean Q-Score: 0.00 > open /home/walter/refine/CEM-1332D4-KP311/S-closed-1332D4/vox- > test/p32-j518-voxel717.ccp4 Opened p32-j518-voxel717.ccp4 as #3, grid size 512,512,512, pixel 0.717, shown at level 0.0147, step 2, values float32 > color #3 #1c71d8ff models > close #1 > qscore #2 toVolume #3 When the ""qscore"" command is called with ""useGui True"", the analysis will be run on the entire model. > ui tool show ""Model-map Q-Score"" > style #2 stick Changed 24700 atom styles > color #2 byhetero > transparency #3 60 Overall mean Q-Score: 0.63 > open /home/walter/refine/CEM-1332D4-KP311/S-closed-1332D4/ward- > structure/embd-48150.mrc Opened embd-48150.mrc as #1, grid size 512,512,512, pixel 0.718, shown at level 0.061, step 2, values float32 > volume #1 level 0.07983 > volume #1 step 1 > open /home/walter/refine/CEM-1332D4-KP311/S-closed-1332D4/ward- > structure/9eli-48150.pdb Chain information for 9eli-48150.pdb #4 --- Chain | Description A B C | No description available > volume #1 level 0.3307 > hide #!2 models > qscore #4 toVolume #1 When the ""qscore"" command is called with ""useGui True"", the analysis will be run on the entire model. > ui tool show ""Model-map Q-Score"" > style #4 stick Changed 25509 atom styles > color #4 byhetero > transparency #1 60 Overall mean Q-Score: 0.60 > qscore #4 toVolume #1 useGui true When the ""qscore"" command is called with ""useGui True"", the analysis will be run on the entire model. > ui tool show ""Model-map Q-Score"" > transparency #1 60 Overall mean Q-Score: 0.60 > style #2 stick Changed 24700 atom styles > color #2 byhetero > style #4 stick Changed 25509 atom styles > color #4 byhetero > volume #3 step 1 > qscore #2 toVolume #3 When the ""qscore"" command is called with ""useGui True"", the analysis will be run on the entire model. > ui tool show ""Model-map Q-Score"" > style #2 stick Changed 24700 atom styles > color #2 byhetero > transparency #3 60 Overall mean Q-Score: 0.63 > qscore #4 toVolume #1 When the ""qscore"" command is called with ""useGui True"", the analysis will be run on the entire model. > ui tool show ""Model-map Q-Score"" > style #4 stick Changed 25509 atom styles > color #4 byhetero > transparency #1 60 Overall mean Q-Score: 0.60 > qscore #2 toVolume #3 When the ""qscore"" command is called with ""useGui True"", the analysis will be run on the entire model. > ui tool show ""Model-map Q-Score"" > style #2 stick Changed 24700 atom styles > color #2 byhetero > transparency #3 60 Overall mean Q-Score: 0.63 Downloading bundle chimerax_isolde-1.10.1-cp311-cp311-linux_x86_64.whl /usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/pkginfo/distribution.py:175: NewMetadataVersion: New metadata version (2.4) higher than latest supported version: parsing as 2.3 warnings.warn(NewMetadataVersion(self.metadata_version)) Installed ChimeraX-Clipper (0.25.2) Installed ChimeraX-ISOLDE (1.10.1) > open /home/walter/refine/CEM-1332D4-KP311/ResolveCryoEM_48/j460-denmod- > voxel717.ccp4 Opened j460-denmod-voxel717.ccp4 as #5, grid size 115,85,139, pixel 0.717,0.717,0.717, shown at level 1.44, step 1, values float32 > open /home/walter/refine/CEM-1332D4-KP311/RealSpaceRefine_50/1332d4-rbd- > vox717_real_space_refined_050.log Install the SEQCROW bundle to open ""Gaussian output file"" format files. Opener for format 'Gaussian output file' is not installed; see log for more info > open /home/walter/refine/CEM-1332D4-KP311/RealSpaceRefine_50/1332d4-rbd- > vox717_real_space_refined_050.pdb Chain information for 1332d4-rbd-vox717_real_space_refined_050.pdb #6 --- Chain | Description B | No description available D | No description available E | No description available > qscore #6 toVolume #5 When the ""qscore"" command is called with ""useGui True"", the analysis will be run on the entire model. > ui tool show ""Model-map Q-Score"" > style #6 stick Changed 3300 atom styles > color #6 byhetero > transparency #5 60 Overall mean Q-Score: 0.59 Traceback (most recent call last): File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site- packages/chimerax/isolde/toolbar.py"", line 332, in _selection_changed_cb self._enable_if_single_peptide_selected_cb() File ""/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site- packages/chimerax/isolde/toolbar.py"", line 318, in _enable_if_single_peptide_selected_cb self.set_enabled(key, enable) File ""/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site- packages/chimerax/isolde/toolbar.py"", line 129, in set_enabled self.session.toolbar.set_enabled(enabled, tab, section, display_name) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/toolbar/manager.py"", line 205, in set_enabled tb.set_enabled(enabled, tab_title, section_title, button_title) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/toolbar/tool.py"", line 271, in set_enabled self.ttb.set_enabled(enabled, tab_title, section_title, button_title) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/tabbedtoolbar.py"", line 559, in set_enabled raise ValueError( ValueError: Didn't find section 'Peptide bond' in tab 'ISOLDE' Error processing trigger ""selection changed"": ValueError: Didn't find section 'Peptide bond' in tab 'ISOLDE' File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/tabbedtoolbar.py"", line 559, in set_enabled raise ValueError( See log for complete Python traceback. > volume #5 level 0.2313 [Repeated 1 time(s)]Traceback (most recent call last): File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site- packages/chimerax/isolde/toolbar.py"", line 332, in _selection_changed_cb self._enable_if_single_peptide_selected_cb() File ""/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site- packages/chimerax/isolde/toolbar.py"", line 318, in _enable_if_single_peptide_selected_cb self.set_enabled(key, enable) File ""/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site- packages/chimerax/isolde/toolbar.py"", line 129, in set_enabled self.session.toolbar.set_enabled(enabled, tab, section, display_name) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/toolbar/manager.py"", line 205, in set_enabled tb.set_enabled(enabled, tab_title, section_title, button_title) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/toolbar/tool.py"", line 271, in set_enabled self.ttb.set_enabled(enabled, tab_title, section_title, button_title) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/tabbedtoolbar.py"", line 559, in set_enabled raise ValueError( ValueError: Didn't find section 'Peptide bond' in tab 'ISOLDE' Error processing trigger ""selection changed"": ValueError: Didn't find section 'Peptide bond' in tab 'ISOLDE' File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/tabbedtoolbar.py"", line 559, in set_enabled raise ValueError( See log for complete Python traceback. > volume #5 level 0.8065 Traceback (most recent call last): File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site- packages/chimerax/isolde/toolbar.py"", line 332, in _selection_changed_cb self._enable_if_single_peptide_selected_cb() File ""/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site- packages/chimerax/isolde/toolbar.py"", line 318, in _enable_if_single_peptide_selected_cb self.set_enabled(key, enable) File ""/home/walter/.local/share/ChimeraX/1.10/lib/python3.11/site- packages/chimerax/isolde/toolbar.py"", line 129, in set_enabled self.session.toolbar.set_enabled(enabled, tab, section, display_name) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/toolbar/manager.py"", line 205, in set_enabled tb.set_enabled(enabled, tab_title, section_title, button_title) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/toolbar/tool.py"", line 271, in set_enabled self.ttb.set_enabled(enabled, tab_title, section_title, button_title) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/tabbedtoolbar.py"", line 559, in set_enabled raise ValueError( ValueError: Didn't find section 'Peptide bond' in tab 'ISOLDE' Error processing trigger ""selection changed"": ValueError: Didn't find section 'Peptide bond' in tab 'ISOLDE' File ""/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/tabbedtoolbar.py"", line 559, in set_enabled raise ValueError( See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 550.54.14 OpenGL renderer: NVIDIA RTX A5000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=gnome XDG_SESSION_DESKTOP=gnome XDG_CURRENT_DESKTOP=GNOME DISPLAY=:3 Manufacturer: To Be Filled By O.E.M. Model: WRX80 Creator R2.0 OS: Rocky Linux 9.6 Architecture: 64bit ELF Virtual Machine: none CPU: 128 AMD Ryzen Threadripper PRO 5995WX 64-Cores Cache Size: 512 KB Memory: total used free shared buff/cache available Mem: 503Gi 18Gi 473Gi 161Mi 15Gi 484Gi Swap: 9Gi 0B 9Gi Graphics: 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102GL [RTX A5000] [10de:2231] (rev a1) Subsystem: NVIDIA Corporation Device [10de:147e] Kernel driver in use: nvidia Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2025.7.14 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 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: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 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: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 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-Clipper: 0.25.2 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 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: 2.5.1 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-ISOLDE: 1.10.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-LinuxSupport: 1.0.1 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 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 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: 1.14.1 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: 1.1.3 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 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: 1.45.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 distro: 1.9.0 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 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: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 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 nvidia-nvjitlink-cu12: 12.9.86 OpenMM: 8.2.0 OpenMM-CUDA-12: 8.2.0 openvr: 1.26.701 packaging: 24.2 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: 25.0.1 pkginfo: 1.11.1 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 PyQt6: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 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: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 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 Third Party limitation Greg Couch all ChimeraX