Opened 2 months ago
Closed 2 months ago
#18470 closed defect (not a bug)
cartoon style modeStrand plank: 'StrandPlank' object has no attribute '_straight_tilt'
Reported by: | Owned by: | Tom Goddard | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Depiction | Version: | |
Keywords: | Cc: | Elaine Meng | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
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
Change History (3)
comment:1 by , 2 months ago
Cc: | added |
---|---|
Component: | Unassigned → Depiction |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → cartoon style modeStrand plank: 'StrandPlank' object has no attribute '_straight_tilt' |
comment:2 by , 2 months ago
Am I missing something? Presumably has not been implemented and thus is not documented. At least, I don't recall ever hearing of its existence.
comment:3 by , 2 months ago
Resolution: | → not a bug |
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Status: | assigned → closed |
The modeStrand option of the cartoon style command was never fully implemented by Conrad when he was working on this 5-10 years ago. The option does not appear in the command usage or documentation so I'm not sure how the reporter found it. Possibly ChatGPT or some similar bot scanned the ChimeraX Python code and found it.
I've removed the modeStrand option from the command. I did not remove the partial code Conrad wrote in case someone in the future wants to fully implement it.
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"modePlank" is not documented on the "cartoon style" help page, nor does it show up in "usage cartoon style"(!).
Reported by Herbert Castillo.