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

[Abhik Mukhopadhyay]

 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>
"
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20211021/a5b66631/attachment.html>