Dear Rex,
if you need to fit only one ligand, and if this fit is the starting
point for further model building, the quickest way to do it is to do a
manual superposition. (calculate - model/fit/refine/ - rotate/translate
zone). If you click twice on an atom of the phenyl ring, your ligand
will rotate around this atom. You then first translate this atom on top
of the corresponding atom of your ligand in place, and then rotate the
ligand to get a perfect fit.
Best,
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of Rex Palmer
Sent: Friday, September 03, 2010 1:44 PM
To: [email protected]
Subject: [ccp4bb] superpositioning two ligands
This is not really protein crystallography but we are trying to
model build a ligand into a protein binding site. A similar ligand is
already in place and we want to replace this by initially superimposing
a phenyl ring which is common to both ligands. We understand that such
superpositioning can be done with eg Quanta but do not have access to
this program. Does anyone know of a downloadable program that we could
use instead?
Rex Palmer
Birkbeck College, London
