VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 25 2003 - 10:32:47 CDT

Dear Yifat,
  You should be aware that if you load multiple PDB files into a
molecule in VMD as a trajectory, the 2nd, and Nth PDB files are
only contributing their atom coordinates, and not atom types etc.
So, if you have PDB files in which that assigned atom type changes
over time, VMD will ignore the changes in subsequent PDB files, and
only the atom name/type assigned in the first PDB file will be the
one used for all trajectory frames. If you are attempting to animate
the results of an ab-initio simulation of some kind, this may cause
you difficulty, but this is still an area where VMD has some growing
to do. If I've misunderstood the problem, please send a followup
email with more details.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu
  

On Mon, Aug 25, 2003 at 06:00:41PM +0300, yifat b wrote:
> Hello,
> I am creating an animation of pdb files with the script "animatepdbs", and
> I have a problem with colors: some atoms in the frames show in different colors
> than they should. When I load a frame as a single molecule, the colors
> are fine - the problem is only at animation. Atoms from the same type (and
> name) don't have the same colors.
> I will appreciate any help.
> Thanks,
> Yifat. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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