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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Hi everyone, <br></div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>I am trying to add hydrogen using the command addh. I am using the command in a python script in this form</div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br></div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">runCommand(<span style="color:rgb(0,128,128);font-weight:bold">"addh spec #0 hbond true"</span>) or <br></div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">runCommand(<span style="color:rgb(0,128,128);font-weight:bold">"addh hbond true"</span>)</div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">both gives a "KeyError: <_molecule.Atom object at 0x7fa2d115c180>"</div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br></div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">But deleting hydrogen with this command works <br></div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br></div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">runCommand(<span style="color:rgb(0,128,128);font-weight:bold">"delete element.H"</span>)</div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br></div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">I have attached the full error report below. Could anyone please help me with this. <br></div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br></div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Thanks in advance,</div><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Abhik<br><pre style="background-color:rgb(255,255,255);color:rgb(8,8,8);font-family:"JetBrains Mono",monospace;font-size:9.8pt"><pre style="background-color:rgb(255,255,255);color:rgb(8,8,8);font-family:"JetBrains Mono",monospace;font-size:9.8pt"><br>"Traceback (most recent call last):<div> File "/home/amukhopadhyay/anaconda3/envs/chimera/bin/pychimera", line 4, in <module></div><div> __import__('pkg_resources').run_script('pychimera==0.2.1', 'pychimera')</div><div> File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/site-packages/pkg_resources/__init__.py", line 666, in run_script</div><div> self.require(requires)[0].run_script(script_name, ns)</div><div> File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1469, in run_script</div><div> exec(script_code, namespace, namespace)</div><div> 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></div><div><br></div><div> File "build/bdist.linux-x86_64/egg/pychimera/__main__.py", line 6, in run</div><div> # All rights reserved. This software provided pursuant to a</div><div> File "build/bdist.linux-x86_64/egg/pychimera/core.py", line 290, in main</div><div> File "build/bdist.linux-x86_64/egg/pychimera/core.py", line 259, in run_cli_options</div><div> File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/runpy.py", line 252, in run_path</div><div> return _run_module_code(code, init_globals, run_name, path_name)</div><div> File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/runpy.py", line 82, in _run_module_code</div><div> mod_name, mod_fname, mod_loader, pkg_name)</div><div> File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/runpy.py", line 72, in _run_code</div><div> exec code in run_globals</div><div> File "chimera_remove_add_hydrogen.py", line 16, in <module></div><div> rc("addh spec #0 hbond true")</div><div> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/chimera/__init__.py", line 2796, in runCommand</div><div> makeCommand(*args, **kw)</div><div> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/Midas/midas_text.py", line 69, in makeCommand</div><div> f(c, args)</div><div> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/ChimeraExtension.py", line 40, in cmdAddH</div><div> specInfo=[("spec", "molecules", "molecules")])</div><div> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/Midas/midas_text.py", line 451, in doExtensionFunc</div><div> extFunc(*tuple(processedArgs), **kw)</div><div> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/__init__.py", line 1006, in cmdAddH</div><div> addHFunc(molecules, inIsolation=inIsolation, **protSchemes)</div><div> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/__init__.py", line 554, in hbondAddHydrogens</div><div> idatmType, hisNs, coordinations, inIsolation)</div><div> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/hbond.py", line 386, in addHydrogens</div><div> if d not in finished and _typeInfo(d).geometry == 4:</div><div> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/hbond.py", line 1403, in _typeInfo</div><div> return typeInfo4Atom[atom]</div><span>KeyError: <_molecule.Atom object at 0x7fa2d115c180></span><br>"</pre></pre></div>
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