AlphaFold Error Plot: list index out of range

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:/Users/shash/Downloads/fold_plsr_lsrr_replicate1/fold_plsr_lsrr_replicate1_model_4.cif

Chain information for fold_plsr_lsrr_replicate1_model_4.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> ui tool show "AlphaFold Error Plot"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py", line 101, in _structure_chosen  
self._guess_pae_file_or_database_id()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py", line 118, in
_guess_pae_file_or_database_id  
pae_path = _matching_pae_file(structure_path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py", line 316, in _matching_pae_file  
mfile = _longest_matching_prefix(filename, pkl_files, min_length = min_length)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py", line 328, in _longest_matching_prefix  
mfilename = m[0][1] if m[0][0] >= min_length and m[0][0] > m[1][0] else None  
~^^^  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py", line 328, in _longest_matching_prefix  
mfilename = m[0][1] if m[0][0] >= min_length and m[0][0] > m[1][0] else None  
~^^^  
  
See log for complete Python traceback.  
  
Must choose path to predicted aligned file  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py", line 62, in <lambda>  
sf.widget.menu().triggered.connect(lambda action, self=self:
self._guess_for_source())  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py", line 132, in _guess_for_source  
pae_path = _matching_pae_file(structure_path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py", line 316, in _matching_pae_file  
mfile = _longest_matching_prefix(filename, pkl_files, min_length = min_length)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py", line 328, in _longest_matching_prefix  
mfilename = m[0][1] if m[0][0] >= min_length and m[0][0] > m[1][0] else None  
~^^^  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\pae.py", line 328, in _longest_matching_prefix  
mfilename = m[0][1] if m[0][0] >= min_length and m[0][0] > m[1][0] else None  
~^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 516.59
OpenGL renderer: NVIDIA GeForce MX350/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_IN.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: windows

Manufacturer: TIMI
Model: Mi NoteBook Horizon Edition 14
OS: Microsoft Windows 11 Home Single Language (Build 26100)
Memory: 8,412,450,816
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.5.1
    build: 1.1.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56
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    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
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    ChimeraX-BugReporter: 1.0.1
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    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
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    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
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    ChimeraX-ImageFormats: 1.2
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    ChimeraX-PDBMatrices: 1.0
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    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.1
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    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.3
    ChimeraX-RenumberResidues: 1.1
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[pett]

Duplicate of #16429