VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 29 2009 - 16:15:05 CDT

Hi,
  When you say "define a box" I assume you mean compute the maxima and
minima of the atom coordinates, yes? If so, then try this:
  set sel [atomselect top "protein"]
  measure minmax $sel

If you need the box padded out by the atom radii, in the newer
VMD 1.8.7 version you can use:
  set sel [atomselect top "protein"]
  measure minmax $sel -withradii

If you want to _draw_ a box on the screen, you can use the minima/maxima
in conjunction with the "draw" or "graphics" commands to do this. See
the VMD User's Guide.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 29, 2009 at 03:06:31PM -0600, Khaled Barakat wrote:
>
> Hi,
>
> I need to use VMD to define a box around my protein that covers all atoms of the macromolecule.
> Would someone help me to write this script?
>
> Thanks,
> Khaled 

-- 
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