id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8207 Fake Atom Error kristen.browne@… Eric Pettersen "{{{ 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) OCICB/OSMO/OD/NIAID/NIH 5601 Fishers Lane, Room 4A60 Rockville, MD 20852 Office 202-253-5228 }}} [attachment:""4hhb-max-hemoglobin.pdb""] [attachment:""hemoglobin-obj03.pdb""] " defect closed normal Structure Editing fixed michal.stolarczyk@… all ChimeraX