VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 16 2010 - 12:23:01 CDT

Edward,
  To accomplish what you have in mind, the easiest method would
be to draw the points as graphics objects with a script, with
each frame in a different molecule. From there, you would animate
the movie using the multimolanim plugin. This would get you past
the issue with varying particle counts, and treating the points as
atoms, etc. Let me know if you need more guidance to get it going.
Ultimately I intend to provide a means of rendering trajectories
of arbitrary particle systems alongside normal molecules in VMD, but
at present the method I describe above is the only thing that's currently
feasible.

Cheers,
  John Stone
 

On Fri, Jul 16, 2010 at 10:54:47AM -0600, Edward Lyman wrote:
> Hi all,
>
> I have a trajectory, but it is not a trajectory of a molecular system.
> Rather it is a trajectory of a bunch of points in a plane that are
> projections of the SASA of a molecular system. I have them stored in xyz
> format, but each frame in my trajectory naturally has a different number
> of points. Also, when I attempt to naively load the entire trajectory into
> vmd, it fails on the second frame with lots of errors about too manty
> bonds, as it tries to connect this points into a molecule.
>
> Is there a simple way to load a stack of, say, 200 snapshots of my points
> and then stack them into an animation? All the scripts I see on the
> website seem to work only for a trajectory that has the same number of
> points in each frame.
>
> Thx,
> Ed 

-- 
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