TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given

[kristen.browne@…]

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)<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

[Eric Pettersen]

This seems to be another microheterogeneity issue. Residue /A:301 (ALA) has only altloc A(!) and /A:302 (GLY) has only altloc B and are in almost the exact same 3D position. I am going to work around this by not having addh use H-bond guidance.

[Eric Pettersen]

Okay, bundle now does not check H-bonds as part of hydrogen addition. Sending wheel separately via email.