From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 11 2003 - 10:26:52 CST

Dear Lars,
  First off, I'd strongly recommend that you use the final released
version of VMD 1.8 rather than the old alpha 29 test version.
If there's some reason that you're having trouble running VMD 1.8
on your machine, please let us know.

That being said, probably the best way to get what you want is to
use the "Dynamic Bonds" representation. Which calculates bonds based
on a distance based bond search heuristic rather than using the
structure given by PSF or other files. That should accomplish what
you have in mind.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 11, 2003 at 05:16:38PM +0100, Lars Bruno Hansen wrote:
>
> dear all,
>
> I have a question regarding the bond connectivity for different
> frames of a molecule.
> I load in coordinates and bonds like, using the python interpreter
>
> molecule.load('psf',psffile,'pdb',pdbfile)
>
> and for the subsequent frames I use
>
> molecule.read(0,'pdb',tmppdbfile)
> molecule.read(0,'psf',tmppsffile)
>
> The coordinates are loaded fine, however it seems like the bonds
> for all frames are allways equal to the last psf file loaded.
> I have tried the 'beg' and 'end' options to the read command
> however this does not seems to have any effects on this.
> I have also tried different order of the two read statements.
>
> I use the front panel animate function to cycle though the
> frames.
>
> Would this works different if I loaded the frames using eg. the
> dcd format.
>
> I use VMD 18a29 on linux.
>
> Any help on this is greatly appreciated,
>
>
> with best regards
> Lars
>
> --
> Lars Bruno Hansen,
> CAMP, Dept. of Physics, Building 307, DTU, DK-2800 Lyngby, Denmark
> Phone: +45 45 25 32 16 Fax: +45 45 93 23 99
> E-mail: lhansen_at_fysik.dtu.dk
>

-- 
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