From: Brian Bennion (bennion1_at_llnl.gov)
Date: Tue Feb 20 2007 - 14:44:17 CST

Hello,

It might be wiser to use another program, but
modeller is very expensive for non academics. If
one only needed to fill in missing loops (small)
or atoms from residues VMD can help. Just make
the atomselections appropriately, "move'" the
template, and then save the resulting coordinates for the missing density.

Then you would have to do some hand editing of a
pdb file to include the appropriate atoms (residues).
Granted it takes a few more steps than modeller,
but for a situation like this it is worth the money.

A more flashy way to do this is use the following
website (unpaid promotion ;) )
http://as2ts.llnl.gov/AS2TS/LGA/lga.html

Brian

At 10:56 AM 2/20/2007, John Stone wrote:
>Hi,
> Yes, I don't think there's a good way of doing this without the
>use of other packages, and it certainly sounds like homology modeling
>is what he's actually after.
>
> John
>
>On Tue, Feb 20, 2007 at 03:43:52PM -0300, Cesar Luis Avila wrote:
> > May be you would prefer to use some homology modelling program like
> > MODELLER for that task.
> > Regards
> > Cesar
> >
> > bertrand russell escribió:
> > >
> > >Dear VMD users,
> > >
> > >I want to superimpose two structures and trying to get the coordinates
> > >of missing atoms in one structure with that of the reference. Is it
> > >possible to do with VMD. It would be of great help if somone could
> > >help me to do this. Many thanks in advance.
> > >--
> > >Live Life; Don't pass it
> > >Bertrand.P.S.Russell
> > >+91-9894398441
>
>--
>NIH Resource for Macromolecular Modeling and Bioinformatics
>Beckman Institute for Advanced Science and Technology
>University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078