hbonds: wrong number of acc_phi_psi() positional arguments

[sajidulghafoor@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Hydrogen bonding not working

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\Rehan Ahmad\\\OneDrive\\\Desktop\\\Chimera job
> learning\\\new website mutated A to G\\\with zones\\\saved modified mutated
> 10 and 10 and 5 and 5.pdb"

Summary of feedback from opening C:\\\Users\\\Rehan
Ahmad\\\OneDrive\\\Desktop\\\Chimera job learning\\\new website mutated A to
G\\\with zones\\\saved modified mutated 10 and 10 and 5 and 5.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK 3DNA v2.4.3-2019apr06, created and maintained by xiangjun@x3dna.org  
  
Start residue of secondary structure not found: HELIX 1 1 GLY R 33 ASN R 36 1
3  
Start residue of secondary structure not found: SHEET 1 1 1 THR V 93 ILE V 98
0  
Start residue of secondary structure not found: SHEET 2 2 1 THR V 107 GLU V
112 0  
Start residue of secondary structure not found: HELIX 1 1 GLY R 33 ASN R 36 1
3  
Start residue of secondary structure not found: SHEET 1 1 1 THR V 93 ILE V 98
0  
7 messages similar to the above omitted  
  
Chain information for saved modified mutated 10 and 10 and 5 and 5.pdb  
---  
Chain | Description  
1.1/0 | No description available  
1.5/0 | No description available  
1.1/A | No description available  
1.2/A | No description available  
1.5/A | No description available  
1.1/R | No description available  
1.1/T | No description available  
1.2/T | No description available  
1.3/T 1.4/T | No description available  
1.5/T | No description available  
1.1/V | No description available  
1.1/a | No description available  
1.1/c | No description available  
1.2/c | No description available  
1.3/c 1.4/c | No description available  
1.5/c | No description available  
1.1/d | No description available  
1.1/i | No description available  
1.2/i | No description available  
1.5/i | No description available  
  

> hbonds reveal true

saved modified mutated 10 and 10 and 5 and 5.pdb #1.1/A C 1677 O3' has bad
number of bonds (3)  

saved modified mutated 10 and 10 and 5 and 5.pdb #1.1/A U 1774 O5' has bad
number of bonds (4)  

saved modified mutated 10 and 10 and 5 and 5.pdb #1.1/A A 1798 O4' has bad
number of bonds (3)  

Skipping possible acceptor with bad geometry: saved modified mutated 10 and 10
and 5 and 5.pdb #1.1/A C 1677 O2  
Wrong number of grandchild atoms for phi/psi acceptor saved modified mutated
10 and 10 and 5 and 5.pdb #1.1/A C 1677 O2  
  
donor: saved modified mutated 10 and 10 and 5 and 5.pdb #1.1/V ARG 42 NH2
acceptor: saved modified mutated 10 and 10 and 5 and 5.pdb #1.1/A A 1798 N3  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\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\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\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1335, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 327, in run  
f(s)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 570, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 513, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\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\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\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 20.19.15.5126
OpenGL renderer: Intel(R) HD Graphics 4600
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 20ANCTO1WW
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 8,458,387,456
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-4910MQ CPU @ 2.90GHz
OSLanguage: en-US

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File attachment: saved modified mutated 10 and 10 and 5 and 5.pdb

saved modified mutated 10 and 10 and 5 and 5.pdb​

[sajidulghafoor@…]

Added by email2trac

[Eric Pettersen]

Hi Sajid,

Your PDB has bad CONECT records, which result in bad / non-physical bonds in the structure. If you delete all the CONECT records from the file before opening it, then hydrogen-bond finding will work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab