From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 22 2004 - 11:40:42 CST

Joshua,
  The answer to your question is about the same as it was when
Rui asked last summer, but I'd like to point out that although there
aren't any built-in features for doing this, one could certainly perform
these calculations in a script by querying the a/b/c/alpha/beta/gamma values
from VMD and doing the pairwise distance calculations for yourself in the
script. The VMD atom selection language doesn't yet incorporate periodic
images, so at present one has to perform these types of 'within' or
distance calculations with custom scripts.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 19, 2004 at 03:10:07PM -0500, Joshua A. Speidel wrote:
> Hello,
>
> Is it possible to specifically select an atom in the periodic images?
> Generally, I would like to write a script to measure the pair-wise distance
> matrix between the 'self' and the image atoms to find the atoms that come
> closest, but don't know how to specify the images... This is similar to a
> previous post (Periodic images J. Rui Rodrigues (Tue Jul 29 2003 - 11:43:23
> CDT) Re: Periodic images Justin Gullingsrud (Tue Jul 29 2003 - 11:38:15 CDT)
> ), and it said there wasn't a method, but I was wondering if it was included
> somehow in the current release.
>
> Thanks,
>
> Josh
>
> Ps. VMD1.8.2; WindowsXP

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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