[Chimera-users] Problem with addh command in Python script

[Eric Pettersen]

Hi Abhik,
	There is something unusual or incorrect about your structure, and Chimera cannot determine one or more of the atom types for atoms in it.  Please use Help→Report A Bug in the Chimera menus to submit a bug report and attach the file for the structure that is producing this error and we can take it from there.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Oct 21, 2021, at 7:05 AM, Abhik Mukhopadhyay via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi everyone, 
> 
> I am trying to add hydrogen using the command addh. I am using the command in a python script in this form
> 
> runCommand("addh spec #0 hbond true") or 
> runCommand("addh hbond true")
> both gives a "KeyError: <_molecule.Atom object at 0x7fa2d115c180>"
> 
> But deleting hydrogen with this command works 
> 
> runCommand("delete element.H")
> 
> I have attached the full error report below. Could anyone please help me with this. 
> 
> Thanks in advance,
> Abhik
> 
> "Traceback (most recent call last):
>   File "/home/amukhopadhyay/anaconda3/envs/chimera/bin/pychimera", line 4, in <module>
>     __import__('pkg_resources').run_script('pychimera==0.2.1', 'pychimera')
>   File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
>     self.require(requires)[0].run_script(script_name, ns)
>   File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1469, in run_script
>     exec(script_code, namespace, namespace)
>   File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/site-packages/pychimera-0.2.1-py2.7.egg/EGG-INFO/scripts/pychimera", line 12, in <module>
> 
>   File "build/bdist.linux-x86_64/egg/pychimera/__main__.py", line 6, in run
>     # All rights reserved.  This software provided pursuant to a
>   File "build/bdist.linux-x86_64/egg/pychimera/core.py", line 290, in main
>   File "build/bdist.linux-x86_64/egg/pychimera/core.py", line 259, in run_cli_options
>   File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/runpy.py", line 252, in run_path
>     return _run_module_code(code, init_globals, run_name, path_name)
>   File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/runpy.py", line 82, in _run_module_code
>     mod_name, mod_fname, mod_loader, pkg_name)
>   File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/runpy.py", line 72, in _run_code
>     exec code in run_globals
>   File "chimera_remove_add_hydrogen.py", line 16, in <module>
>     rc("addh spec #0 hbond true")
>   File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/chimera/__init__.py", line 2796, in runCommand
>     makeCommand(*args, **kw)
>   File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/Midas/midas_text.py", line 69, in makeCommand
>     f(c, args)
>   File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/ChimeraExtension.py", line 40, in cmdAddH
>     specInfo=[("spec", "molecules", "molecules")])
>   File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/Midas/midas_text.py", line 451, in doExtensionFunc
>     extFunc(*tuple(processedArgs), **kw)
>   File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/__init__.py", line 1006, in cmdAddH
>     addHFunc(molecules, inIsolation=inIsolation, **protSchemes)
>   File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/__init__.py", line 554, in hbondAddHydrogens
>     idatmType, hisNs, coordinations, inIsolation)
>   File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/hbond.py", line 386, in addHydrogens
>     if d not in finished and _typeInfo(d).geometry == 4:
>   File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/hbond.py", line 1403, in _typeInfo
>     return typeInfo4Atom[atom]
> KeyError: <_molecule.Atom object at 0x7fa2d115c180>
> "
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