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: hsc43@… 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 Eric Pettersen, 2 months ago

Cc: Elaine Meng added
Component: UnassignedDepiction
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissioncartoon style modeStrand plank: 'StrandPlank' object has no attribute '_straight_tilt'

"modePlank" is not documented on the "cartoon style" help page, nor does it show up in "usage cartoon style"(!).

Reported by Herbert Castillo.

comment:2 by Elaine Meng, 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 Tom Goddard, 2 months ago

Resolution: not a bug
Status: assignedclosed

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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