VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 01 2001 - 13:13:47 CST

Dear Tom,
  Though VMD will read multi-frame PDB files as a trajectory, it does
not store any per-timestep information other than the atom coordinates
(yet). Recently a number of people have been asking how to do this
sort of thing, but the simple answer is that VMD doesn't yet provide
support for per-timestep bonds, coloring, etc. The only way to change
colors on a per-timestep basis in the current versions of the software
is to write a script that re-colors the molecule via the "beta" field,
changing the colors every frame. An example of coloring by script is
shown in the "betacolor_distance" example here:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.7/ug/node178.html
If you combine that script with a simple loop to drive
the trajectory animation, you should be able to assign any colors
you want on a per-frame basis. In the long run, we are considering
teaching VMD to store much more information (optionally) per-timestep
so that scripts like these are no longer necessary.

Let us know if you have other questions.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 31, 2001 at 06:24:04PM -0500, tom keyes wrote:
> I thought I had solved the problem of animating a series of trajectories
> with a frame-dependent coloring scheme. A colleague showed me that I could
> just concatenate N pdb files in the format:
> MODEL 1
> frame1.pdb
> ENDMDL
> etc
> MODEL n
> framen.pdb
> ENDMDL
> etc
> MODEL N
> frameN.pdb
> ENDMDL
>
> and I was excited to find that VMD would read that file, with .pdb
> extension, as having N frames and happily animate them. However I put my
> color variable in the beta field, different for each molecule in each
> frame, and the molecules don't change color through the animation. I'd
> guess that VMD is assigning the colors based on the first frame, just as if
> it were reading a single pdb file plus a crd file. Is there any way to get
> VMD to read the color on each frame. What's the simplest way to animate
> with time-dependent coloring?
>
> TIA
> Tom
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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