All hydrogen names for taken

[wangyue1@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
ValueError: All hydrogen names for /L NH2 10 N taken!


I couldn't addh for some atoms. I don't know how to fix it.

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:/OX-V2R project/data processing/final/OT-V2R-Gqset-11111-coot-7.pdb"

Chain information for OT-V2R-Gqset-11111-coot-7.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
G | No description available  
L | No description available  
N | No description available  
  

> hide cartoons

> show cartoons

> hide atoms

> style stick

Changed 8138 atom styles  

> show atoms

> color byhetero

> set bgColor white

> addh

Summary of feedback from adding hydrogens to OT-V2R-Gqset-11111-coot-7.pdb #1  
---  
notes | No usable SEQRES records for OT-V2R-Gqset-11111-coot-7.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for OT-V2R-Gqset-11111-coot-7.pdb (#1) chain B;
guessing termini instead  
No usable SEQRES records for OT-V2R-Gqset-11111-coot-7.pdb (#1) chain C;
guessing termini instead  
No usable SEQRES records for OT-V2R-Gqset-11111-coot-7.pdb (#1) chain G;
guessing termini instead  
No usable SEQRES records for OT-V2R-Gqset-11111-coot-7.pdb (#1) chain L;
guessing termini instead  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A ASP 33, /B GLU 3, /C LEU
12, /G THR 6, /L CYS 1, /N GLN 1  
Chain-initial residues that are not actual N termini: /C THR 204, /C ASN 264  
Chain-final residues that are actual C termini: /A LEU 308  
Chain-final residues that are not actual C termini: /B ASN 340, /C VAL 394, /C
ILE 62, /C ASP 252, /G ARG 62, /L GLY 9, /N SER 128  
892 hydrogen bonds  
  
Traceback (most recent call last):  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 764, in add_hydrogens  
_attach_hydrogens(a, altloc_hpos_info, bonding_info)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 909, in _attach_hydrogens  
add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens,
naming_schema)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 910, in add_altloc_hyds  
h = new_hydrogen(atom, i+1, total_hydrogens, naming_schema,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 949, in new_hydrogen  
new_h = add_atom(_h_name(parent_atom, h_num, total_hydrogens, naming_schema),
"H",  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 1046, in _h_name  
raise ValueError("All hydrogen names for %s taken!" % atom)  
ValueError: All hydrogen names for /L NH2 10 N taken!  
  
ValueError: All hydrogen names for /L NH2 10 N taken!  
  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-packages\chimerax\addh\cmd.py",
line 1046, in _h_name  
raise ValueError("All hydrogen names for %s taken!" % atom)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 516.94
OpenGL renderer: NVIDIA GeForce GTX 1650 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: IPASON
Model:  
OS: Microsoft Windows 11 家庭中文版 (Build 22631)
Memory: 25,720,573,952
MaxProcessMemory: 137,438,953,344
CPU: 6 AMD Ryzen 5 3500X 6-Core Processor             
OSLanguage: zh-CN

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[Eric Pettersen]

Hi Yue,

Thanks for reporting this problem. ChimeraX is not correctly estimating the atom type for the N in /L NH2, causing it to try to add too many hydrogens to it. You can correct the atom type (before running addh) with the command: "setattr :nh2@n a idatm_type Npl".

--Eric

Eric Pettersen
UCSF Computer Graphics Lab