Foldseek sequences: IndexError

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.9.dev202408090049 (2024-08-09 00:49:16 UTC)
Description
Foldseek sequences button produces this error.

Log:
UCSF ChimeraX version: 1.9.dev202408090049 (2024-08-09)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/goddard/Downloads/ChimeraX/Foldseek/fold_cch1_mid1_model_0.cif_B/fold_cch1_mid1_model_0.cif_B_pdb100.m8
> format foldseek

Summary of feedback from opening
/Users/goddard/Downloads/ChimeraX/Foldseek/fold_cch1_mid1_model_0.cif_B/fold_cch1_mid1_model_0.cif_B_pdb100.m8  
---  
notes |   
  
  
| Chain information for fold_cch1_mid1_model_0.cif #1  
  
---  
  
  
Chain  
| Description  
  
  
  
  
  
  
A  
| .  
  
  
  
  
B  
| .  
  
  
  
  
  
Computing secondary structure  
Foldseek search for similar structures to /B in pdb100 found 64 hits  
  

> foldseek sequences

Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Aug 9
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/foldseek/gui.py", line 262, in _show_sequences  
run(self.session, 'foldseek sequences')  
File "/Users/goddard/Desktop/ChimeraX Aug 9
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/Desktop/ChimeraX Aug 9
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/Desktop/ChimeraX Aug 9
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/foldseek/sequences.py", line 37, in foldseek_sequences  
fsp = FoldseekSequencePlot(session, fp.results, order = order,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/goddard/Desktop/ChimeraX Aug 9
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/foldseek/sequences.py", line 90, in __init__  
results.set_coverage_attribute()  
File "/Users/goddard/Desktop/ChimeraX Aug 9
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/foldseek/foldseek.py", line 962, in set_coverage_attribute  
count = count_nonzero(alignment_array[1:,ai])  
~~~~~~~~~~~~~~~^^^^^^^  
IndexError: index 358 is out of bounds for axis 1 with size 358  
  
IndexError: index 358 is out of bounds for axis 1 with size 358  
  
File "/Users/goddard/Desktop/ChimeraX Aug 9
2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/foldseek/foldseek.py", line 962, in set_coverage_attribute  
count = count_nonzero(alignment_array[1:,ai])  
~~~~~~~~~~~~~~~^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Ultra
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: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 performance and 8 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 56 days, 17 hours, 7 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


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    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
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    ChimeraX-DeepSSETracer: 1.1
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    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-Foldseek: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
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[Tom Goddard]

Fixed.

The code did not properly handle the case where a query residue has no hit residue aligned.