superimposing molecules

Geoff Barton gjb at bioch.ox.ac.uk
Tue Dec 10 06:02:51 EST 1996


Ira Ropson wrote:
> 
> Hi world,
> 
> I would like to superimpose three structures in the same family of
> proteins for comparison purposes for a paper I'm writing on the folding
> of proteins having considerable sequence heterogeneity but very similar
> X-ray structures. The proteins are intestinal fatty acid binding
> protein (131 aa), cellular retinol binding protein 2 (133 aa), and
> cellular retinoic acid binding protein (136 aa). I can superimpose them
> by eye useing Berkeley RASMAC, and they look pretty good, but I would
> like to do a better job by mathematically fitting the backbones of
> these proteins to each other. I have insightII available to me on an
> SGI, but it states that you have to have the same number of atoms to do
> the superposition. Does anyone know of an easy way to do this
> (preferably without spending any money)? Is there an easy way to do
> this in insightII?
> 
> Thanks,
> Ira Ropson
> iropson at bcmic.hmc.psu.edu
> If I had time for a fancy Sig file I problably wouldn't have a job.

STAMP (Structural Alignment of Multiple Proteins) will do what you want.
See:  ftp://geoff.biop.ox.ac.uk/README as well as our WWW pages.
The manual is on-line at
http://geoff.biop.ox.ac.uk/manuals/stamp.4.0/stamp.html
Geoff.

-- 
Geoffrey J. Barton, Laboratory of Molecular Biophysics, University of
Oxford, 
Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K.
mailto:geoff.barton at ox.ac.uk, Tel: +44 1865 275368, Fax: +44 1865
510454, 
ftp://geoff.biop.ox.ac.uk, http://geoff.biop.ox.ac.uk



More information about the Molmodel mailing list