VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 07 2008 - 13:22:02 CDT

Hi,
  There's no built-in feature for doing this, but you could
write a short Tcl script to do this sort of thing. You might
also check and see if this is built into the PBCTools plugin,
and/or ask Olaf Lenz about adding such a feature if there's a
chance that others would also find it useful.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 29, 2008 at 09:27:39AM -0700, Brian Kidd wrote:
> hello vmd users,
>
> i would like to calculate the distance between atoms in two different
> periodic images. the basic code logic would look something like:
>
> 1. create image of starting molecule, say +X.
> 3. create atomselection of set in the image
> 3. create atomselection of set in original molecule
> 4. calculate distances between atoms in the two set
>
> i noticed that there is a command called showperiodic. can i use this
> command to create a tcl variable that is a new atomselection command
> of a periodic image? if so, how would i do that? if not, is there a
> way to do this in VMD?
>
> i'm basically asking for help with steps 1 and 2 outlined above
>
> thanks,
> -brian 

-- 
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