VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 24 2003 - 22:04:47 CST

Hi,
  I'd like to take this opportunity to say that if some individuals would
like to test an alpha version of VMD which contains the new periodic image
display feature, I would be willing to make a test version available so
that we can get feedback on it from people working with periodic systems.
For convenience sake, I'd be primarily interested in providing Unix versions
such a test release, but if you use Windows or MacOS X and are willing to
give us good feedback, I'll consider building test versions for those
platforms as well.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 24, 2003 at 08:31:07PM -0600, Justin Gullingsrud wrote:
> Ioana,
>
> At present, the only way to do this is to load the pdb file twice, then
> translate or move one of the molecules along the periodic cell vector.
> We have code now in the current development version of VMD to do exactly
> what you describe, but it has not been released. We'll announce as usual
> on vmd-l when beta versions of the new version of VMD are available for
> testing.
>
> To move a molecule, create an atom selection and use the moveby command:
> set sel [atomselect top all]
> $sel moveby {30 0 0}
>
> Cheers,
> Justin
>
> On Mon, Feb 24, 2003 at 05:19:32PM -0800, Ioana Cozmuta wrote:
> > Hi,
> >
> > I tried to find a similar subject on the vmd web page but was unsuccesful.
> > I would like to load a PDB file that is a periodic boundary condition
> > structure and vizualize more than one unit cell in various directions. Is
> > there already a tcl routine developed in vmd to do this, any suggestions?
> >
> > Thank you in advance,
> > Ioana
>
> --
>
> Justin Gullingsrud 3111 Beckman Institute 217-244-8946
> I been dropping the new science, and I be kicking the new knowledge,
> and I'm seeing to a degree that you can't get in college. -- b.boys 

-- 
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