H-bonds: acc_phi_psi() takes 8 positional arguments but 9 were given

[garimagarima082@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22623
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
H bonding interactions not showing

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:/PLK11/Docking/2RKUL28docking/stableL28.pdb

Chain information for stableL28.pdb #1  
---  
Chain | Description  
A | No description available  
  

> set bgColor white

> lighting soft

> select /A

2972 atoms, 2862 bonds, 294 residues, 1 model selected  

> rainbow sel

> select clear

> select ::name="UNL"

41 atoms, 45 bonds, 1 residue, 1 model selected  

> select ::name="UNL"

41 atoms, 45 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

/A SER 99 OG has bad number of bonds (3)  

Skipping possible acceptor with bad geometry: /A CYS 318 O  
Wrong number of grandchild atoms for phi/psi acceptor /A CYS 318 O  
  
Skipping possible acceptor with bad geometry: /A VAL 114 O  
Wrong number of grandchild atoms for phi/psi acceptor /A VAL 114 O  
  
Skipping possible acceptor with bad geometry: /A ARG 144 O  
Wrong number of grandchild atoms for phi/psi acceptor /A ARG 144 O  
  
Skipping possible acceptor with bad geometry: /A ASP 194 O  
Wrong number of grandchild atoms for phi/psi acceptor /A ASP 194 O  
  
Skipping possible acceptor with bad geometry: /A SER 326 O  
Wrong number of grandchild atoms for phi/psi acceptor /A SER 326 O  
  
Skipping possible acceptor with bad geometry: /A ASP 187 O  
Wrong number of grandchild atoms for phi/psi acceptor /A ASP 187 O  
  
Skipping possible acceptor with bad geometry: /A LEU 286 O  
Wrong number of grandchild atoms for phi/psi acceptor /A LEU 286 O  
  
Skipping possible acceptor with bad geometry: /A ASP 187 O  
Wrong number of grandchild atoms for phi/psi acceptor /A ASP 187 O  
  
Skipping possible acceptor with bad geometry: /A LYS 61 O  
Wrong number of grandchild atoms for phi/psi acceptor /A LYS 61 O  
  
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: /A VAL 114 O  
Wrong number of grandchild atoms for phi/psi acceptor /A VAL 114 O  
  
Skipping possible acceptor with bad geometry: /A SER 99 O  
Wrong number of grandchild atoms for phi/psi acceptor /A SER 99 O  
  
[Repeated 2 time(s)]Skipping possible acceptor with bad geometry: /A ARG 144 O  
Wrong number of grandchild atoms for phi/psi acceptor /A ARG 144 O  
  
Skipping possible acceptor with bad geometry: /A ASP 187 O  
Wrong number of grandchild atoms for phi/psi acceptor /A ASP 187 O  
  
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: /A ASP 194 O  
Wrong number of grandchild atoms for phi/psi acceptor /A ASP 194 O  
  
Skipping possible acceptor with bad geometry: /A LEU 286 O  
Wrong number of grandchild atoms for phi/psi acceptor /A LEU 286 O  
  
Skipping possible acceptor with bad geometry: /A CYS 318 O  
Wrong number of grandchild atoms for phi/psi acceptor /A CYS 318 O  
  
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: /A VAL 114 O  
Wrong number of grandchild atoms for phi/psi acceptor /A VAL 114 O  
  
Skipping possible acceptor with bad geometry: /A ASP 194 O  
Wrong number of grandchild atoms for phi/psi acceptor /A ASP 194 O  
  
[Repeated 1 time(s)]donor: /A ARG 51 NH1 acceptor: /A ARG 51 NE  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 327, in run  
f(s)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\hbonds\cmd.py", line 83, in cmd_hbonds  
result = hb_func(session, struct_info, dist_slop=dist_slop,
angle_slop=angle_slop, **base_kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\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  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.2004
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_IN.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: Dell Inc.
Model: Inspiron 3493
OS: Microsoft Windows 11 Home Single Language (Build 22623)
Memory: 8,345,964,544
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i3-1005G1 CPU @ 1.20GHz
OSLanguage: en-US

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File attachment: stableL28.pdb

stableL28.pdb​

[garimagarima082@…]

Added by email2trac

[Eric Pettersen]

Hi Garima,

I don't know how you generated this PDB file, but it has a lot of problems. For instance, in residue 326 there are two copies of each and every atom(!). Perhaps they were supposed to be alternate locations, but if so the alternate location indicators are missing. ChimeraX will not be able to find H-bonds for a problematic structure like this.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab