VMD-L Mailing List

From: yifat b (yifatb_at_fh.huji.ac.il)
Date: Tue Aug 26 2003 - 05:25:18 CDT

Thanks John,
Yes, that was my problem, I'll have to work it out somehow.
Yifat.

On Mon, 25 Aug 2003, John Stone wrote:

>
> 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.
>
>