Subject: Re: CCL:rebuilding a molecule after changing the coordinates of a subsection

From: Konrad Hinsen <hinsen$at$cnrs-orleans.fr>
Date: Mon, 22 Dec 2003 10:09:36 +0100

On Monday 22 December 2003 00:12, Alex Sutcliffe wrote:

> I have a molecule in pdb format. I have chopped out a fragment and tried
> docking it to another molecule. So now I have new coordinates for just
> the subsection. I would like to be able to rebuild the rest of the
> molecule in relation to the new coordinates. Any suggestions on the best
> way to do this?

Assuming that the subsection hasn't been overly deformed in the docking 
process, I'd try this: Do a least-squares superposition of the subsection 
> from the initial to the modified conformation. Apply the resulting rigid-body 
transformation to the rest of the molecule. Put the two pieces together again 
and do some energy minimization to get a presentable molecule.
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From: szilva{at}computer.org
Date: Mon, 22 Dec 2003 08:36:14 +0100 (CET)

> I would like to be able to rebuild the rest of the

AFAIK Swiss-PDB can superpose your proteins:

http://us.expasy.org/spdbv/text/toolmenu.htm

or the commercial tool MOE. There are many other software I had never used
for superposition.

Szilva