<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Abhik,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>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.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 21, 2021, at 7:05 AM, Abhik Mukhopadhyay via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Hi everyone, <br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class="">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;" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">runCommand(<span style="color:rgb(0,128,128);font-weight:bold" class="">"addh spec #0 hbond true"</span>) or <br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">runCommand(<span style="color:rgb(0,128,128);font-weight:bold" class="">"addh hbond true"</span>)</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">both gives a "KeyError: <_molecule.Atom object at 0x7fa2d115c180>"</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">But deleting hydrogen with this command works <br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">runCommand(<span style="color:rgb(0,128,128);font-weight:bold" class="">"delete element.H"</span>)</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">I have attached the full error report below. Could anyone please help me with this. <br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Thanks in advance,</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Abhik<br class=""><pre style="background-color:rgb(255,255,255);color:rgb(8,8,8);font-family:"JetBrains Mono",monospace;font-size:9.8pt" class=""><pre style="background-color:rgb(255,255,255);color:rgb(8,8,8);font-family:"JetBrains Mono",monospace;font-size:9.8pt" class=""><br class="">"Traceback (most recent call last):<div class=""> File "/home/amukhopadhyay/anaconda3/envs/chimera/bin/pychimera", line 4, in <module></div><div class=""> __import__('pkg_resources').run_script('pychimera==0.2.1', 'pychimera')</div><div class=""> File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/site-packages/pkg_resources/__init__.py", line 666, in run_script</div><div class=""> self.require(requires)[0].run_script(script_name, ns)</div><div class=""> File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1469, in run_script</div><div class=""> exec(script_code, namespace, namespace)</div><div class=""> 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 class=""><br class=""></div><div class=""> File "build/bdist.linux-x86_64/egg/pychimera/__main__.py", line 6, in run</div><div class=""> # All rights reserved. This software provided pursuant to a</div><div class=""> File "build/bdist.linux-x86_64/egg/pychimera/core.py", line 290, in main</div><div class=""> File "build/bdist.linux-x86_64/egg/pychimera/core.py", line 259, in run_cli_options</div><div class=""> File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/runpy.py", line 252, in run_path</div><div class=""> return _run_module_code(code, init_globals, run_name, path_name)</div><div class=""> File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/runpy.py", line 82, in _run_module_code</div><div class=""> mod_name, mod_fname, mod_loader, pkg_name)</div><div class=""> File "/home/amukhopadhyay/anaconda3/envs/chimera/lib/python2.7/runpy.py", line 72, in _run_code</div><div class=""> exec code in run_globals</div><div class=""> File "chimera_remove_add_hydrogen.py", line 16, in <module></div><div class=""> rc("addh spec #0 hbond true")</div><div class=""> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/chimera/__init__.py", line 2796, in runCommand</div><div class=""> makeCommand(*args, **kw)</div><div class=""> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/Midas/midas_text.py", line 69, in makeCommand</div><div class=""> f(c, args)</div><div class=""> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/ChimeraExtension.py", line 40, in cmdAddH</div><div class=""> specInfo=[("spec", "molecules", "molecules")])</div><div class=""> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/Midas/midas_text.py", line 451, in doExtensionFunc</div><div class=""> extFunc(*tuple(processedArgs), **kw)</div><div class=""> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/__init__.py", line 1006, in cmdAddH</div><div class=""> addHFunc(molecules, inIsolation=inIsolation, **protSchemes)</div><div class=""> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/__init__.py", line 554, in hbondAddHydrogens</div><div class=""> idatmType, hisNs, coordinations, inIsolation)</div><div class=""> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/hbond.py", line 386, in addHydrogens</div><div class=""> if d not in finished and _typeInfo(d).geometry == 4:</div><div class=""> File "/home/amukhopadhyay/.local/UCSF-Chimera64-1.15rc/share/AddH/hbond.py", line 1403, in _typeInfo</div><div class=""> return typeInfo4Atom[atom]</div><span class="">KeyError: <_molecule.Atom object at 0x7fa2d115c180></span><br class="">"</pre></pre></div>
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