hbonds: wrong number of acc_phi_psi() positional arguments

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC)
Description
Just ran dockprep on a structure obtained from GPCRmd

Log:
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\laasfeld\Downloads\11012_dyn_106.pdb format pdb

Chain information for 11012_dyn_106.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select /A

4679 atoms, 4742 bonds, 294 residues, 1 model selected  

> select ~sel & ##selected

85642 atoms, 67166 bonds, 18478 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> dockprep

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
Swapping /A ALA 26 to ALA  
/A CYS 231: phi -70.2, psi none trans  
Swapping /A GLY 313 to GLY  
donor: /A CYS 1 N acceptor: /A CYS 231 O  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 170, in dock_prep_cmd  
dock_prep_caller(session, structures, memorization=memorize, nogui=True, **kw)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 96, in prep  
swap_aa(session, targets, "same", rot_lib=style)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\swap_res\swap_res.py", line 122, in swap_aa  
process_hbonds(session, res, by_alt_loc, False, None, None, hbond_relax,  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\swap_res\swap_res.py", line 805, in process_hbonds  
hbonds = { hb: color for hb in find_hbonds(session, target_models,
intra_model=False,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 513.36
OpenGL renderer: Quadro T1000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: et_EE.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: windows

Manufacturer: LENOVO
Model: 20ST0064MX
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 16,919,126,016
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
OSLanguage: en-US

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