"alphafold pae true" does not guard against starting tool in nogui mode

[mbopf@…]

I’m getting an error in NIH3D when submitting an AlphaFold QS job, but only when running on the server, not locally on my Mac. The error is:

prefect.ShellTask:shell.py:151 NIH3D FATAL ERROR: Could not open P00520 from alphafold pae true: 'UI' object has no attribute 'main_window'

I’ve attached the debug output from our run. I do not have access to any of the output files at this time.

This was running under Ubuntu 20.04 on our test server. The UniProtID was P00520. This runs fine on my Mac and produces what looks like valid output.

Thanks,
Mike


Mike Bopf, M.S. (he/him)
Python Developer
Bioinformatics Software Section
Contractor, MSC | Guidehouse
Bioinformatics and Computational Biosciences Branch<https://www.niaid.nih.gov/research/bioinformatics-computational-biosciences-branch>
NIH/NIAID/OD/OSMO/OCICB
Office: 240-899-8397 | Mobile: 240-961-0015
mbopf@nih.gov<mailto:mbopf@nih.gov>

ChimeraX_window_issue.txt​

[mbopf@…]

Added by email2trac

[Eric Pettersen]

There are situations, like this one, where the end user just wants to be able to run a subsequent "alphafold pae colorDomains" command.

[Tom Goddard]

Here is the full traceback from running the following command in nogui mode

cmd> open P00520 fromDatabase alphafold pae true autoStyle false

Executing: open P00520 fromDatabase alphafold pae true autoStyle false
Fetching AlphaFold database settings, 0.000609 of 0.000609 Mbytes received
Fetching AlphaFold P00520, 0.205 of 0.205 Mbytes received
Fetching AlphaFold PAE P00520, 0.345 of 0.345 Mbytes received
Summary of feedback from opening P00520 fetched from alphafold  
---  
_notes_ | Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold P00520 from
https://alphafold.ebi.ac.uk/files/AF-P00520-F1-model_v4.cif  
Fetching compressed AlphaFold PAE P00520 from
https://alphafold.ebi.ac.uk/files/AF-P00520-F1-predicted_aligned_error_v4.json  
  


Unexpected exception, save your work and exit:

Traceback (most recent call last):
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/nogui.py", line 232, in execute
    self._cmd.run(text)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3209, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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 "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3209, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 166, in provider_open
    models, status = collated_open(session, database_name, ident,
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 513, in collated_open
    return remember_data_format()
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484, in remember_data_format
    models, status = func(*func_args, **func_kw)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/__init__.py", line 85, in fetch
    return alphafold_fetch(session, ident, ignore_cache=ignore_cache,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/fetch.py", line 72, in alphafold_fetch
    alphafold_pae(session, structure = models[0], uniprot_id = uniprot_id, version = version,
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py", line 1433, in alphafold_pae
    p = AlphaFoldPAEPlot(session, 'AlphaFold Predicted Aligned Error', pae,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py", line 438, in __init__
    tw = MainToolWindow(self)
         ^^^^^^^^^^^^^^^^^^^^
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 2387, in __init__
    super().__init__(tool_instance, tool_instance.display_name, **kw)
  File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 2116, in __init__
    mw = ui.main_window
         ^^^^^^^^^^^^^^
AttributeError: 'UI' object has no attribute 'main_window'

[Tom Goddard]

Fixed in daily build dated June 26, 2024 or later.

I made the alphafold pae code not try to show the plot in nogui mode.