Fake Atom Error

[kristen.browne@…]

Am seeing the below error for three different entries:
A quicksubmit of PDB 4HHB and the two attached files.

Let us know if this is fixable or something we should try to deal with on our end.

Thanks!
...
add_nonstandard_res_charges(session, res_list, estimate_net_charge(res_list[0].atoms),
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/add_charge/charge.py", line 289, in add_nonstandard_res_charges
session.change_tracker.add_modified(a, "charge changed")
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 2153, in add_modified
f(self._inst_to_int(modded), modded._c_pointer, reason.encode('utf-8'))
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 2238, in _inst_to_int
raise AssertionError("Unknown class for change tracking: %s" % inst.__class__.__name__)
AssertionError: Unknown class for change tracking: FakeAtom
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__main__.py", line 747, in init
run(sess, 'runscript %s' % script)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/runscript.py", line 38, in runscript
open_python_script(session, open(script_file, 'rb'), script_file, argv=argv)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/scripting.py", line 90, in open_python_script
raise UserError('Error opening python file %s' % stream.name)
chimerax.core.errors.UserError: Error opening python file /usr/local/lib/python3.9/site-packages/nih_3d_workflows/flows/chimerax_flow/chimera_x_scripts/cx_unified.py


Kristen Browne, MSc, MscBMC
Contractor - MSC, Inc. | A Guidehouse Company
3D Modeling and Biovisualization Specialist
Bioinformatics and Computational Biosciences Branch (BCBB)<https://www.niaid.nih.gov/research/bioinformatics-computational-biosciences-branch>
OCICB/OSMO/OD/NIAID/NIH

5601 Fishers Lane, Room 4A60
Rockville, MD 20852
Office 202-253-5228

4hhb-max-hemoglobin.pdb​

hemoglobin-obj03.pdb​

[kristen.browne@…]

Added by email2trac

[kristen.browne@…]

Added by email2trac

[pett]

I have submitted a pull request on cx_unified.py that fixes this. Something must have become slightly confused between my local clones and GitHub, because GitHub claims the pull request contains four commits. Michal, if this pull request proves problematic to integrate, let me know and I'll try to generate a cleaner pull request.