AlphaFold Error Plot: list index out of range

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8.dev202403290055 (2024-03-29 00:55:10 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.8.dev202403290055 (2024-03-29)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:/Users/Mitarbeiter/Downloads/fold_rh1_arr2_m1/fold_rh1_arr2_m1_model_0.cif

Chain information for fold_rh1_arr2_m1_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> hide atoms

> show atoms

> hide atoms

> show atoms

> 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.  
  
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.  
  

> close

> open C:/Users/Mitarbeiter/Desktop/Arr2_Rh1_M1.cif

Chain information for Arr2_Rh1_M1.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file C:/Users/Mitarbeiter/Desktop\\\Protein_1_rank_1.json

Number of residues in structure "Arr2_Rh1_M1.cif #1" is 774 which does not
match PAE matrix size 1359.  
  
This can happen if chains were deleted from the AlphaFold model or if the PAE
data was applied to a structure that was not the one predicted by AlphaFold.
Use the full-length AlphaFold model to show predicted aligned error.  

> open
> C:/Users/Mitarbeiter/Downloads/fold_rh1_arr2_m1/fold_rh1_arr2_m1_summary_confidences_0.json

Install the ArtiaX bundle to open "Copick Picks file" format files.  
Opener for format 'Copick Picks file' is not installed; see log for more info  

> open
> C:/Users/Mitarbeiter/Downloads/fold_rh1_arr2_m1/fold_rh1_arr2_m1_summary_confidences_0.json

Install the ArtiaX bundle to open "Copick Picks file" format files.  
Opener for format 'Copick Picks file' is not installed; see log for more info  
Downloading bundle ChimeraX_ArtiaX-0.5.0-py3-none-any.whl  
[Repeated 1 time(s)]Bundle installation canceled  
Downloading bundle ChimeraX_ArtiaX-0.5.0-py3-none-any.whl  
  

> open
> C:/Users/Mitarbeiter/Downloads/fold_rh1_arr2_m1/fold_rh1_arr2_m1_summary_confidences_0.json

Install the ArtiaX bundle to open "Copick Picks file" format files.  
Opener for format 'Copick Picks file' is not installed; see log for more info  
Downloading bundle ChimeraX_ArtiaX-0.5.0-py3-none-any.whl  
Installed ChimeraX-ArtiaX (0.5.0)  

> open
> C:/Users/Mitarbeiter/Downloads/fold_rh1_arr2_m1/fold_rh1_arr2_m1_summary_confidences_0.json

Summary of feedback from opening
C:/Users/Mitarbeiter/Downloads/fold_rh1_arr2_m1/fold_rh1_arr2_m1_summary_confidences_0.json  
---  
notes | Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black  
    lighting depthCue false  
    camera ortho

  
  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 54, in event  
if self.handle_drag_and_drop(event):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 124, in handle_drag_and_drop  
mw.dropEvent(event)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py",
line 662, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py",
line 2027, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Mitarbeiter\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\artiax\io\formats.py", line 25, in open  
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Mitarbeiter\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\artiax\io\io.py", line 104, in open_particle_list  
data = formats[format_name].particle_data(  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Mitarbeiter\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\artiax\io\Copick\CopickParticleData.py", line 154, in
__init__  
super().__init__(session, file_name, oripix=oripix, trapix=trapix,
additional_files=additional_files)  
File "C:\Users\Mitarbeiter\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\artiax\io\ParticleData.py", line 489, in __init__  
self.read_file()  
File "C:\Users\Mitarbeiter\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\artiax\io\Copick\CopickParticleData.py", line 161, in
read_file  
self.picks = CopickPicksFile(**data)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Mitarbeiter\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\pydantic\v1\main.py", line 341, in __init__  
raise validation_error  
pydantic.v1.error_wrappers.ValidationError: 3 validation errors for
CopickPicksFile  
pickable_object_name  
field required (type=value_error.missing)  
user_id  
field required (type=value_error.missing)  
session_id  
field required (type=value_error.missing)  
  
pydantic.v1.error_wrappers.ValidationError: 3 validation errors for
CopickPicksFile  
pickable_object_name  
field required (type=value_error.missing)  
user_id  
field required (type=value_error.missing)  
session_id  
field required (type=value_error.missing)  
  
File "C:\Users\Mitarbeiter\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\pydantic\v1\main.py", line 341, in __init__  
raise validation_error  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.2115
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel

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

Manufacturer: HP
Model: HP EliteDesk 800 G5 TWR
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 16,943,194,112
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-9500 CPU @ 3.00GHz
OSLanguage: de-DE

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    annotated-types: 0.7.0
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    ChimeraX-AlignmentMatrices: 2.1
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    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
    WMI: 1.5.1

[Tom Goddard]

Fixed long ago in ChimeraX 1.8.