AlphaFold Error Plot: IndexError: list index out of range

[vincent.yao.1@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8.dev202403200605 (2024-03-20 06:05:36 UTC)
Description
opened Tools/Structure Prediction/Alphafold Error Plot with an Alphafold 3 predicted .cif file

Log:
UCSF ChimeraX version: 1.8.dev202403200605 (2024-03-20)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "G:\\\My Drive\\\Vanderbilt IGP\\\1 Tansey Lab\\\Projects\\\23-04-11
> Alphafold\\\2 MYC box IIIa IIIb IV fragment 2HYB AF\\\11-MYC-MBD4\\\cxs 11
> myc-mbd4.cxs"

Log from Wed Oct 9 15:55:04 2024

> lighting gentle

> set bgColor white

> set silhouettes true

> show cartoons

> hide atoms

UCSF ChimeraX version: 1.8.dev202403200605 (2024-03-20)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "G:\\\My Drive\\\Vanderbilt IGP\\\1 Tansey Lab\\\Projects\\\23-04-11
> Alphafold\\\2 MYC box IIIa IIIb IV fragment 2HYB AF\\\11-MYC-
> MBD4\\\fold_2024_10_09_11_18_11_myc_mbd4_model_0.cif"

Chain information for fold_2024_10_09_11_18_11_myc_mbd4_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> color bychain

> preset custom "myc central portion renumber"

Using preset: Custom / MYC Central Portion Renumber  
169 residues renumbered  
Preset expands to these ChimeraX commands:

    
    
    renumber /A seqStart 151

  

> preset custom vypreset

Using preset: Custom / Vypreset  
Preset expands to these ChimeraX commands:

    
    
    lighting gentle
    set bgcolor white
    set silhouettes true
    set silhouettedepth 0.02
    

  

> 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.  
  

QWindowsWindow::setGeometry: Unable to set geometry 645x150+1118+782 (frame:
667x206+1107+737) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 639x133+1121+796 (frame:
661x189+1110+751) margins: 11, 45, 11, 11 minimum size: 430x99 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=667, y=205)))  

> alphafold pae #1 file "G:/My Drive/Vanderbilt IGP/1 Tansey
> Lab/Projects/23-04-11 Alphafold/2 MYC box IIIa IIIb IV fragment 2HYB
> AF/11-MYC-MBD4/fold_2024_10_09_11_18_11_myc_mbd4_full_data_0.json"

QWindowsWindow::setGeometry: Unable to set geometry 758x836+1062+440 (frame:
780x892+1051+395) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 752x819+1065+454 (frame:
774x875+1054+409) margins: 11, 45, 11, 11 minimum size: 469x128 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=726, y=248)))  

> alphafold contacts /a toResidues /b distance 5 maxPae 10

> select /a:275-288

111 atoms, 111 bonds, 14 residues, 1 model selected  

> preset custom "label preset"

Using preset: Custom / Label Preset  
Preset expands to these ChimeraX commands:

    
    
    label (#!1 & sel) text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
    label bgColor white
    label height 1.4
    

  

> save "G:/My Drive/Vanderbilt IGP/1 Tansey Lab/Projects/23-04-11 Alphafold/2
> MYC box IIIa IIIb IV fragment 2HYB AF/11-MYC-MBD4/cxs 11 myc-mbd4.cxs"

——— End of log from Wed Oct 9 15:55:04 2024 ———

opened ChimeraX session  

> select sequence eeidvvsvekrqap

111 atoms, 111 bonds, 14 residues, 1 model selected  

> ~label sel residues

> 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.  
  

QWindowsWindow::setGeometry: Unable to set geometry 645x150+1118+782 (frame:
667x206+1107+737) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 639x133+1121+796 (frame:
661x189+1110+751) margins: 11, 45, 11, 11 minimum size: 430x99 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=667, y=205)))  

QWindowsWindow::setGeometry: Unable to set geometry 900x713+990+501 (frame:
922x769+979+456) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 894x696+993+515 (frame: 916x752+982+470)
margins: 11, 45, 11, 11 minimum size: 600x321 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=922, y=538)))  




OpenGL version: 3.3.0 - Build 31.0.101.5081
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

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

Manufacturer: LENOVO
Model: 20QA000GUS
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 16,885,276,672
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1160G7 @ 1.20GHz
OSLanguage: en-US

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
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    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
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    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
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    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202403200605
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
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    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
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    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
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    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
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    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
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    ChimeraX-Mask: 1.0.2
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    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
    WMI: 1.5.1

[Tom Goddard]

This was fixed 5 months ago (bug #15143). Get ChimeraX 1.8 to avoid this error in Alphafold Error Plot.