id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18470 cartoon style modeStrand plank: 'StrandPlank' object has no attribute '_straight_tilt' hsc43@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.26100 ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC) Description cartoon #1 cartoon style #1 modeHelix tube cartoon style #1 modeStrand plank Log: UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open > ""C:\Users\eyepl\Downloads\fold_2025_08_18_13_36_e_coli_aer_dimer_with_2_fad\E > coli Aer Dimer Domain Annotated.cxs"" format session Log from Mon Aug 18 14:16:27 2025UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold > alphafold search > MSSHPYVTQQNTPLADDTTLMSTTDLQSYITHANDTFVQVSGYTLQELQGQPHNMVRHPDMPKAAFADMWFTLKKGEPWSGIVKNRRKNGDHYWVRANAVPMVREGKISGYMSIRTRATDEEIAAVEPLYKALNAGRTSKRIHKGLVVRKGWLGKLPSLPLRWRARGVMTLMFILLAAMLWFVAAPVVTYILCALVVLLASACFEWQIVRPIENVAHQALKVATGERNSVEHLNRSDELGLTLRAVGQLGLMCRWLINDVSSQVSSVRNGSETLAKGTDELNEHTQQTVDNVQQTVATMNQMAASVKQNSATASAADKLSITASNAAVQGGEAMTTVIKTMDDIADSTQRIGTITSLINDIAFQTNILALNAAVEAARAGEQGKGFAVVAGEVRHLASRSANAANDIRKLIDASADKVQSGSQQVHAAGRTMEDIVAQVKNVTQLIAQISHSTLEQADGLSSLTRAVDELNLITQKNAELVEESAQVSAMVKHRASRLEDAVTVLH > open > C:\Users\eyepl\Downloads\fold_2024_09_25_11_12\fold_2024_09_25_11_12_model_0.cif > format mmcif Chain information for fold_2024_09_25_11_12_model_0.cif #1 --- Chain | Description A B | . Computing secondary structure > select /A:1-506 3861 atoms, 3917 bonds, 506 residues, 1 model selected > select /B:1-506 3861 atoms, 3917 bonds, 506 residues, 1 model selected > close > open C:/Users/eyepl/Downloads/fold_2025_08_18_11_15_e_coli_aer_dimer.zip Unrecognized file suffix '.zip' > open > C:/Users/eyepl/Downloads/fold_2025_08_18_11_15_e_coli_aer_dimer/fold_2025_08_18_11_15_e_coli_aer_dimer_model_0.cif Chain information for fold_2025_08_18_11_15_e_coli_aer_dimer_model_0.cif #1 --- Chain | Description A B | . Computing secondary structure > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file > C:/Users/eyepl/Downloads/fold_2025_08_18_11_15_e_coli_aer_dimer\\\fold_2025_08_18_11_15_e_coli_aer_dimer_full_data_0.json > color /A lime > color /A/B:1 lime > color /B:4-506 #1/C:1 magenta > color /A:1-251 lime > color /B:290-446 magenta > color /A:1-272 lime > color /A:302-456 magenta > color /A:283-490 lime > color /A:506/B:1-317 magenta > color /A:371-503 lime > color /B:380-506 #1/C:1@PA magenta > color /A:7-494 lime > color > #1/C:1@C2A,N3A,C4A,N1,C2,O2,N3,C4,O4,C4X,N5,C5X,C6,C7,C7M,C8,C8M,C9,C9A,N10,C10,C1',C2' > magenta > alphafold pae #1 colorDomains true > undo Undo failed, probably because structures have been modified. > color /A:279-486 lime > color bfactor #1 palette alphafold 7775 atoms, 1013 residues, atom bfactor range 22.5 to 97.2 > color bfactor #1 palette alphafold 7775 atoms, 1013 residues, atom bfactor range 22.5 to 97.2 > set bgColor white > view > cartoon > lighting soft > set bgColor white > lighting soft > color cornflowerblue #1/A Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color salmon #1/B Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color cornflowerblue #1/A Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select /A 3861 atoms, 3917 bonds, 506 residues, 1 model selected > select clear > select #1 & /A 3861 atoms, 3917 bonds, 506 residues, 1 model selected > color sel cornflowerblue > select clear > select #1 & /B 3861 atoms, 3917 bonds, 506 residues, 1 model selected > color sel salmon > select clear > color bfactor #1 palette alphafold 7775 atoms, 1013 residues, atom bfactor range 22.5 to 97.2 > cartoon colorByChain true Expected an atoms specifier or a keyword > select #1 & (/A,:1-120) Expected a keyword > color sel gold > select #1 & (/B,:1-120) Expected a keyword > color sel gold > select clear > select #1 & (/A,:1-120) Expected a keyword > color sel gold > color dodgerblue #1/A:1-120 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color dodgerblue #1/B:1-120 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color dodgerblue #1.1/A:1-120 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color dodgerblue #1.0/A:1-120 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color dodgerblue #./A:1-120 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color dodgerblue #1.1:1-120 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color red #1.1:1-50 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color red #1:1-50 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color red #1.:1-50 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color red #1.1:1-50 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1/A cornflowerblue > color #1/B salmon > color #1/A:1-120 dodgerblue > color #1/B:1-120 dodgerblue > color #1/A:179-199 orange > color #1/A:225-245 orange > color #1/B:179-199 orange > color #1/B:225-245 orange > color #1/A:248-309 forestgreen > color #1/B:248-309 forestgreen > color #1/A cornflowerblue > color #1/B salmon > color #1/A black > color #1/b black > color #1/A:15-144 dodgerblue > color #1/B:15-144 dodgerblue > color #1/A:171-200 orange > color #1/B:171-200 orange > style stick #1/A:171-200 Expected a keyword > style stick #1/B:171-200 Expected a keyword > transparency 20 #1/A:171-200 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 20 #1/B:171-200 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1/A:206-248 forestgreen > color #1/B:206-248 forestgreen > color #1/A:263-492 magenta > color #1/B:263-492 magenta > close > open > C:\Users\eyepl\Downloads\fold_2025_08_18_11_15_e_coli_aer_dimer\fold_2025_08_18_11_15_e_coli_aer_dimer_model_0.cif > format mmcif Chain information for fold_2025_08_18_11_15_e_coli_aer_dimer_model_0.cif #1 --- Chain | Description A B | . Computing secondary structure > close > open > C:/Users/eyepl/Downloads/fold_2025_08_18_13_36_e_coli_aer_dimer_with_2_fad/fold_2025_08_18_13_36_e_coli_aer_dimer_with_2_fad_model_0.cif Chain information for fold_2025_08_18_13_36_e_coli_aer_dimer_with_2_fad_model_0.cif #1 --- Chain | Description A B | . Computing secondary structure > color #1/A black > color #1/B black > color #1/A:15-144 dodgerblue > color #1/B:15-144 dodgerblue > color #1/A:171-200 orange > color #1/B:171-200 orange > color #1/A:206-248 forestgreen > color #1/B:206-248 forestgreen > color #1:15-144 dodgerblue > color #1:171-200 orange > color #1:206-248 forestgreen > color #1:263-492 magenta > label #1/A:80 text PAS color dodgerblue height 2 > label #1/B:80 text PAS color dodgerblue height 2 > set bgColor black > set bgColor white > hide #!1 models > show #!1 models > label delete #1 > label #1/A:135 text PAS height 36 color dodgerblue > label #1/B:135 text PAS height 36 color dodgerblue > label #1/B:135 text PAS height 24 color dodgerblue > label #1/B:135 text PAS height 12 color dodgerblue > label #1/A:135 text PAS height 12 color dodgerblue > label delete #1B Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > label delete #1B Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > label delete #1/B > label #1/A:178 text TM height 12 color orange > label #1/A:163 text HAMP height 12 color forestgreen > label #1/A:308 text Kinase control domain height 12 color magenta Expected a keyword > label #1/A:308 text KCD height 12 color magenta > 2dlabels create PAS_A text PAS color dodgerblue size 32 bgColor white > opacity 0.4 Expected a keyword > save > ""C:/Users/eyepl/Downloads/fold_2025_08_18_13_36_e_coli_aer_dimer_with_2_fad/E > coli Aer Dimer Domain Annotated.cxs"" ——— End of log from Mon Aug 18 14:16:27 2025 ——— > view name session-start opened ChimeraX session > cartoon #1 > cartoon style #1 modeHelix tube > cartoon style #1 modeStrand plank 6 oxygens of 43 atoms in 6 residues Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.10\bin\Lib\site- packages\chimerax\core\triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10\bin\Lib\site- packages\chimerax\atomic\structure.py"", line 1940, in _update_graphics_if_needed s[i].update_graphics_if_needed() File ""C:\Program Files\ChimeraX 1.10\bin\Lib\site- packages\chimerax\atomic\structure.py"", line 380, in update_graphics_if_needed self._create_ribbon_graphics() File ""C:\Program Files\ChimeraX 1.10\bin\Lib\site- packages\chimerax\atomic\structure.py"", line 690, in _create_ribbon_graphics ribbons_drawing.compute_ribbons(self) File ""C:\Program Files\ChimeraX 1.10\bin\Lib\site- packages\chimerax\atomic\ribbon.py"", line 630, in compute_ribbons _make_ribbon_graphics(structure, self) File ""C:\Program Files\ChimeraX 1.10\bin\Lib\site- packages\chimerax\atomic\ribbon.py"", line 130, in _make_ribbon_graphics _smooth_ribbon(residues, coords, guides, helix_ranges, sheet_ranges, File ""C:\Program Files\ChimeraX 1.10\bin\Lib\site- packages\chimerax\atomic\ribbon.py"", line 969, in _smooth_ribbon _arc_strand(rlist, coords, guides, start, end) File ""C:\Program Files\ChimeraX 1.10\bin\Lib\site- packages\chimerax\atomic\ribbon.py"", line 1113, in _arc_strand sp = StrandPlank(coords[start:end], oxygens.coords) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.10\bin\Lib\site- packages\chimerax\atomic\sse.py"", line 488, in __init__ self._straight_optimize() File ""C:\Program Files\ChimeraX 1.10\bin\Lib\site- packages\chimerax\atomic\sse.py"", line 566, in _straight_optimize self.width_vector, self.thickness_vector = self._straight_tilt() ^^^^^^^^^^^^^^^^^^^ AttributeError: 'StrandPlank' object has no attribute '_straight_tilt' Error processing trigger ""graphics update"": AttributeError: 'StrandPlank' object has no attribute '_straight_tilt' File ""C:\Program Files\ChimeraX 1.10\bin\Lib\site- packages\chimerax\atomic\sse.py"", line 566, in _straight_optimize self.width_vector, self.thickness_vector = self._straight_tilt() ^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 - Build 32.0.101.6913 OpenGL renderer: Intel(R) Graphics OpenGL vendor: Intel Python: 3.11.4 Locale: en_US.cp1252 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: windows Manufacturer: LENOVO Model: 21KE001WUS OS: Microsoft Windows 11 Pro (Build 26100) Memory: 33,782,067,200 MaxProcessMemory: 137,438,953,344 CPU: 14 Intel(R) Core(TM) Ultra 7 155U OSLanguage: en-US Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 asttokens: 3.0.0 auditwheel: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.5.0 build: 1.2.2.post1 certifi: 2025.6.15 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: 14.1.18 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-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 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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 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: 1.1.2 ChimeraX-PubChem: 2.2 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 comtypes: 1.4.10 contourpy: 1.3.2 coverage: 7.9.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.4 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: 4.4.4 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-cuda-cupti-cu12: 12.9.79 nvidia-cuda-nvcc-cu12: 12.9.86 nvidia-cuda-nvrtc-cu12: 12.9.86 nvidia-cuda-runtime-cu12: 12.9.79 nvidia-cufft-cu12: 11.4.1.4 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 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 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 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-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 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 pywin32: 310 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: 4.14.0 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 WMI: 1.5.1 }}} " defect closed normal Depiction not a bug Elaine Meng all ChimeraX