AddH: type_info_for_atom KeyError

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10rc202505090204 (2025-05-09 02:04:01 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10rc202505090204 (2025-05-09)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> //wsl.localhost/Ubuntu-22.04/home/almem/vScreenML2_env/ugl_8qer_wat/8qer_waters.pdb

Chain information for 8qer_waters.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select ::name="HOH"

18 atoms, 12 bonds, 6 residues, 1 model selected  

> show sel target ab

> select H

2997 atoms, 419 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /B:615@O

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /B:631@O

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select /B:644@O

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> open C:/Users/Alberto/Desktop/UGL_fixed.mol2

Opened UGL_fixed.mol2 containing 1 structure (27 atoms, 27 bonds)  

> ui tool show "Add Hydrogens"

> addh #1 inIsolation false

Summary of feedback from adding hydrogens to 8qer_waters.pdb #1  
---  
notes | Termini for 8qer_waters.pdb (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 8qer_waters.pdb #1/A SER
0  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 8qer_waters.pdb #1/A PHE
412  
449 hydrogen bonds  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10rc202505090204\bin\Lib\site-
packages\chimerax\addh\tool.py", line 186, in add_h  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.10rc202505090204\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202505090204\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202505090204\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 "C:\Program Files\ChimeraX 1.10rc202505090204\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 "C:\Program Files\ChimeraX 1.10rc202505090204\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 401, in add_hydrogens  
if a not in finished and _type_info(a).geometry == 4:  
^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202505090204\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 1364, in _type_info  
return type_info_for_atom[atom]  
~~~~~~~~~~~~~~~~~~^^^^^^  
KeyError: <chimerax.atomic.molobject.Atom object at 0x00000241697EB150>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX 1.10rc202505090204\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 1364, in _type_info  
return type_info_for_atom[atom]  
~~~~~~~~~~~~~~~~~~^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.101.2079
OpenGL renderer: Intel(R) Iris(R) Plus Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: it_IT.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: HP
Model: HP 250 G8 Notebook PC
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 16,951,066,624
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-1065G7 CPU @ 1.30GHz
OSLanguage: it-IT

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[Eric Pettersen]

Somehow an acceptor is not in type_info_for_atom. Would need the structure file to reproduce.