VMD-L Mailing List

From: Karsten Suhre (Karsten.Suhre_at_igs.cnrs-mrs.fr)
Date: Thu Jul 29 2004 - 01:43:24 CDT

Dear Min,

> I have two static frames of a loop structure, one is in an open form,
> the other is in closed form. I would like to make an animation which
> shows the transformation movement from open to closed. I am wondering if
> VMD can do this. The effect should be something similar to
> view_change_render, but instead of moving between different views, it shows
> the movement between two loop structures.

.. depending how much "biological reality" you want to give to your mouvement,
rather than just morphing one form into the other, you can compute a
transition by using normal mode analysis (NMA). We have a web-server (ElNemo)
at

http://igs-server.cnrs-mrs.fr/elnemo/

that allows to do that. If you enter two structures (open and closed forms)
ElNemo will indicate whcih normal mode(s) describe the protein movement and
to which degree. ElNemo also generates PDB files with several frames, that
you can download and visualize as an animation in vmd (see http://
igs-server.cnrs-mrs.fr/elnemo/examples.html for example that I generated
using VMD).

I hope this helps,

Kind regards, Karsten.