"cartoon style modeStrand plank": NameError: name 'ribbons_drawing' is not defined

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.9.dev202409261947 (2024-09-26 19:47:38 UTC)
Description
Entered into command line: "car style modes plank"

Error:
Error processing trigger "graphics update":
NameError: name 'ribbons_drawing' is not defined

File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 1119, in _arc_strand
name = ribbons_drawing.structure_name + " strand guide " + str(start)
^^^^^^^^^^^^^^^

See log for complete Python traceback.



Log:
Startup Messages  
---  
warning | QCoreApplication::postEvent: Unexpected null receiver  
note | available bundle cache has not been initialized yet  
  

> ui tool show Matchmaker

UCSF ChimeraX version: 1.9.dev202409261947 (2024-09-26)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/Kyrellos/Library/Mobile
> Documents/com~apple~CloudDocs/Desktop/UCSF/Kortemme_Lab/PKS/valerolactam_experiment/valerolactam_experiment_AF3_preds/nema/fold_nema1_009_model_3.pdb"

Chain information for fold_nema1_009_model_3.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Computing secondary structure  

> cartoon style modeStrand plank

9 oxygens of 62 atoms in 9 residues  
slope 0.145071371588096  
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/sse.py:707: FutureWarning: `rcond` parameter will
change to the default of machine precision times ``max(M, N)`` where M and N
are the input matrix dimensions.  
To use the future default and silence this warning we advise to pass
`rcond=None`, to keep using the old, explicitly pass `rcond=-1`.  
m, _, _, _ = lstsq(x[2:-2,newaxis], y[2:-2])  
lstsq [0.18188082]  

QCoreApplication::exec: The event loop is already running  

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1906, in
_update_graphics_if_needed  
s[i].update_graphics_if_needed()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 363, in update_graphics_if_needed  
self._create_ribbon_graphics()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 673, in _create_ribbon_graphics  
ribbons_drawing.compute_ribbons(self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 630, in compute_ribbons  
_make_ribbon_graphics(structure, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 130, in _make_ribbon_graphics  
_smooth_ribbon(residues, coords, guides, helix_ranges, sheet_ranges,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 969, in _smooth_ribbon  
_arc_strand(rlist, coords, guides, start, end)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 1119, in _arc_strand  
name = ribbons_drawing.structure_name + " strand guide " + str(start)  
^^^^^^^^^^^^^^^  
NameError: name 'ribbons_drawing' is not defined  
  
Error processing trigger "graphics update":  
NameError: name 'ribbons_drawing' is not defined  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 1119, in _arc_strand  
name = ribbons_drawing.structure_name + " strand guide " + str(start)  
^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: MNEH3LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 10 days, 21 hours, 19 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2412M:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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    ChimeraX-Core: 1.9.dev202409261947
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
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    ChimeraX-DeepMutationalScan: 1.0
    ChimeraX-Dicom: 1.2.5
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    ChimeraX-Dssp: 2.0
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    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
    ChimeraX-Help: 1.3
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    ChimeraX-IHM: 1.1
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    ChimeraX-IMOD: 1.0
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    ChimeraX-LookingGlass: 1.1
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    ChimeraX-Mole: 1.0
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    ChimeraX-PubChem: 2.2
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    ChimeraX-RotamerLibsRichardson: 2.0
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    ChimeraX-Segger: 1.0
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    ChimeraX-VIPERdb: 1.0
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    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
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    colorama: 0.4.6
    comm: 0.2.2
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    Cython: 3.0.10
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    imagecodecs: 2024.6.1
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[pett]

Also, testing with 2x57 that same command produces: 'StrandPlank' object has no attribute '_straight_tilt'

[Tom Goddard]

Not sure how the reporter found the "modeStrand" option of the cartoon style command. That is an option Conrad started to implement and never completed. It is not documented in the User Guide and does not appear in the command usage. It does not show up in a google search. I think the only way you could find it is by looking at the code. It is currently listed as a hidden option in the code. I could remove it as an option. But I think no one will ever find it and keeping it as a hidden option may improve the chances of someone in the future trying to complete the implementation.