id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8199 TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given kristen.browne@… Eric Pettersen "{{{ This is a quicksubmit for PDB 4YKJ ... File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/addh/cmd.py"", line 66, in cmd_addh add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/addh/cmd.py"", line 173, in hbond_add_hydrogens add_hydrogens(session, atoms, type_info_for_atom, naming_schemas, hydrogen_totals, File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/addh/hbond.py"", line 248, in add_hydrogens hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop, angle_slop=rec_angle_slop) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/hbonds/hbond.py"", line 603, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given 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 Command failed with exit code 70 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 }}} " defect closed normal Structure Analysis fixed all ChimeraX