Hi there...

If you want to generate your morph-pdbs with sensible geometry, try this script:
http://www.molmovdb.org/molmovdb/morph/download/morph_dist.inp

It requires CNS, but if you have start and end, it interpolates smoothly, using all atoms, without distorting geometry of side chains and so on.

Can give very nice results, and is fully compatible with pymol.

D

On 28/02/07, Clara Marco <cmarco@ibv.csic.es> wrote:
Hi!
I'm trying to build a morphing movie to show the transition between
two conformational states of a protein. I've run morphing with
program LSQMAN, which has generated intermediate pdb files between
start.pdb and end.pdb.The problem is that to avoid geometry
distortions I've used a LSQMAN option that only uses CA's and few
side chains (selected by proximity of the ligand that induces the
conformational change), and now, the intermediate pdbs only have CA's
coordinates.
Is there any possibility to represent these pdb's with pymol
(cartoon/ribbon)? I've tried it but it only represents points/spheres
corresponding to the CA's.
If not, does anyone know how to calculate morphing intermediate pdb's
suitable to be represented with pymol?
Thank you very much.
Clara
Clara Marco-Marin
Instituto de Biomedicina de Valencia
Consejo Superior de Investigaciones Cientificas
C/Jaime Roig, 11
46010 Valencia
Espaņa


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