VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Sat Jun 22 2002 - 17:07:56 CDT

Hi,

On Sat, Jun 22, 2002 at 02:21:01PM -0700, Jennifer Young wrote:
> User List,
>
> I want to produce an animation from a series of pdb and psf files. The
> problem is that each file has a different number of atoms. I have used the
> 'brute force' method of picking a maximum number of atoms and filling out
> each file with dummy atoms to produce a constant number of atoms which
> works. Is there any other way to do this? Another file format? Some
> scripting trick?

With scripting of course anything is possible ;) However, your method of
adding additional dummy atoms to the files is about as good as you can do;
VMD requires that all timesteps in a molecule have the same number of atoms.
Another approach you could take would be to load each psf/pdb as a separate
molecule, then produce an animation by successively turning one molecule on
at a time:

foreach molid [molinfo list] {
  mol off all
  mol on $molid
  # do stuff here
}

Does that help? I'm not sure what you want to do with your animation, but if
you just want to produce a "canned" show that loops over all molecules, that
should do it. Let us know if you have further questions.

Cheers,

Justin

>
> Thanks,
> Jennifer
>
> ******************************************
> Jennifer A. Young
> Lawrence Livermore National Laboratory
> Chemistry and Chemical Engineering Division
> P.O. Box 808, L-091
> Livermore, CA 94550
>
> phone: (925) 422-3673
> fax: (925) 424-2626
>
> ******************************************** 

-- 
Justin Gullingsrud      3111 Beckman Institute
H: (217) 384-4220       I got a million ideas that I ain't even rocked yet...
W: (217) 244-8946       -- Mike D