Cif file open issue

[Xuewu.Zhang@…]

Hi ChimeraX developers:
I got the following errors when trying to open the attached cif file from AlphaFold3 in ChimeraX 1.11 on my MacBook M4. I also tried 1.12, got the same errors. However, it opened without any error in ChimeraX 1.9 in Linux.





Traceback (most recent call last):
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1732, in _report_model_info
    chain = chain_lookup[chain_id]
            ~~~~~~~~~~~~^^^^^^^^^^
KeyError: 'C'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 816, in dropEvent
    _open_dropped_file(self.session, p)
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
    run(session, 'open %s' % FileNameArg.unparse(path))
  File "/Applications/ChimeraX-1.11.1.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 "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3237, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 132, in cmd_open
    models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0]
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3237, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 297, in provider_open
    session.models.add(opened_models)
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py", line 827, in add
    m.added_to_session(session)
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1409, in added_to_session
    self._report_model_info(session)
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1751, in _report_model_info
    res = nc_residues[int(seq_id)]
                      ^^^^^^^^^^^
ValueError: invalid literal for int() with base 10: '.'

ValueError: invalid literal for int() with base 10: '.'

File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1751, in _report_model_info
res = nc_residues[int(seq_id)]
^^^^^^^^^^^

See log for complete Python traceback.

Computing secondary structure



Thanks,


Xuewu Zhang


________________________________

UT Southwestern

Medical Center

The future of medicine, today.

sp_Q9NZC2_TREM2_HUMAN_model.cif​

[Xuewu.Zhang@…]

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