Editing Cealign plugin (section)

=== The Function SimpAlign() is not found ===
'''Problem''': Running CE Align gives the following error message:
<source lang="python">
PyMOL>cealign 1CLL,1GGZ
Traceback (most recent call last):
  File "C:\Program Files (x86)\DeLano Scientific\PyMOL/modules\pymol\parser.py", line 203, in parse
    result=apply(kw[nest][0],args[nest],kw_args[nest])
  File "py24/Lib/cealign.py", line 177, in cealign
    curScore = simpAlign( matA, matB, mol1, mol2, stored.mol1, stored.mol2, align=0, L=len(matA) )
NameError: global name 'simpAlign' is not defined
</source>
I am running PyMOL v. 0.99rc6 on Win XP Professional x64 edition version 2003 sp2 and have followed the windows install procedure as described above.

'''Answer''': This simply means that PyMOL couldn't find the simplAlign function.  To let PyMOL know about this, you must run the following commands before running [[cealign]]:
<source lang="python">
run /your/path/to/cealign/qkabsch.py
run /your/path/to/cealign/cealign.py
</source>
but most people that use cealign would just put these two lines in their '''.pymolrc''' file.