VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 15 2004 - 16:24:29 CDT

Hi,
  If what you have in mind is to create a new PDB/PSF pair from
several repeated unit cells, it should be possible with a bit of
psfgen scripting. I don't have an example script, but I suspect
the simple method would be to make an atom selection for all of the
pieces that wouldn't overlap (i.e. if some of the structure is already
replicated at all, you'd need to fix that in the selection, otherwise
you'd just use "all"), then perform several translations, writing out
each new pdb file. From there, you'd load the pdb files into psfgen
merging them into a single structure, and emit a new pdb/psf pair
for the full system. If you look through the manual and some of the
scripts I've posted for merging structures, you ought to be able to
put it together. Let us know if you need more help.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 15, 2004 at 02:19:11PM -0400, Yang Yang wrote:
> Hello everyone,
>
> I am a newcomer to VMD. I've got a question for help.
>
> I have a pdb and a psf files for a unit cell. I use the "Periodic
> Tab" under "Graphical Reperesentation" menu to replicate it in some
> direction to form a periodic image. Now I am wondering if there
> exists a way of generating a pdb and a psf files for this new image
> by using VMD?
>
> Thank you.
>
> Young
>
> --
> Research Assistant,CFD Lab,tel.(269-276-3433),
> Department of Mechanical and Aeronautical Engineering
> College of Engineering and Applied Sciences
> Western Michigan University 

-- 
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