AddH adding hydrogen to terminal C?

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8.dev202403072314 (2024-03-07 23:14:14 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.8.dev202403072314 (2024-03-07)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/Laptop Valley/Desktop/dockingd/pure protein 1ro5.pdb"

Summary of feedback from opening C:/Users/Laptop Valley/Desktop/dockingd/pure
protein 1ro5.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK BIOVIA PDB file  
  
Ignored bad PDB record found on line 2  
REMARK Created: 2024-01-09T15:55:24Z  
  
Chain information for pure protein 1ro5.pdb #1  
---  
Chain | Description  
A | No description available  
  
32 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select main

3142 atoms, 3171 bonds, 197 residues, 1 model selected  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A ARG 197: phi -121.0, psi none trans  
Applying ARG rotamer (chi angles: -67.7 179.1 -179.0 176.3) to /A ARG 197  
Summary of feedback from adding hydrogens to pure protein 1ro5.pdb #1  
---  
notes | No usable SEQRES records for pure protein 1ro5.pdb (#1) chain A;
guessing termini instead  
Chain-initial residues that are actual N termini: /A GLY 397  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ARG 197  
Chain-final residues that are not actual C termini:  
153 hydrogen bonds  
12 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 129, in add_standard_charges  
h.charge, h.gaff_type = hyd_charge_type_data[(h.residue.amber_name,
heavy.name.lower())]  
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
KeyError: ('ARG', 'c')  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\add_charge\tool.py", line 120, in add_charges  
self._finish_add_charge(residues)  
File "C:\Program Files\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\add_charge\tool.py", line 146, in _finish_add_charge  
non_std = add_standard_charges(self.session, residues=residues, **params)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 131, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to atom that should not have hydrogens
(%s)"  
chimerax.add_charge.charge.ChargeError: Hydrogen /A ARG 197 HC bonded to atom
that should not have hydrogens (/A ARG 197 C)  
  
chimerax.add_charge.charge.ChargeError: Hydrogen /A ARG 197 HC bonded to atom
that should not have hydrogens (/A ARG 197 C)  
  
File "C:\Program Files\ChimeraX\ChimeraX\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 131, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to atom that should not have hydrogens
(%s)"  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8854
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel

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

Manufacturer: HP
Model: HP ProBook 440 G5
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 8,475,856,896
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
OSLanguage: en-US

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[Eric Pettersen]

I can't get AddH to add the bad hydrogen; maybe this file had it initially?