VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 09 2002 - 14:24:36 CDT

Dear Paul,
  Yes, you should be able to use the atomselect "get" and "set"
methods to manipulate the atom coordinates of a structure, to create
any interpolation you like between two coordinate frames. You could
load the coordinate frames in multiple times to give you a trajectory
of the number of frames you want, then use the atomselect commands to
modify the coordinates for the interpolated frames. Once they are
all setup the way you want, you could write out the trajectory as
a file (to make future re-loading or modifications easier/faster)
and you could then use the vmd movie making scripts to process this
animation for you. Here's an example of a script that does
processing along these lines:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/trajectory_smooth/

Let us know if you have more questions,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 09, 2002 at 02:12:49PM -0500, Paul Hubbard wrote:
> Hi,
>
> I would like to make a short animation where a protein ligand undergoes
> large torsion about 2 bonds. I have the before and after crystal
> structures, but would like the inbetween ones. Strictly speaking, I'm
> not trying to do a simulation, just interpolation. I was wondering if
> VMD can do this - if so, could someone please give me some pointers as
> to how to do this.
>
> Thanks
>
> AGS
>
> --
> Paul Hubbard
> Dept. of Biochemistry
> Medical College of Wisconsin
> Phone: 414-456 4305
> Fax: 414-456 6510
> URL: iris9.biochem.mcw.edu
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078