VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 15 2007 - 23:02:17 CST

Cesar,
  The existing "measure minmax" only calculates the bounding box that
contains the atom centers. There isn't any built-in feature that
does the exact calculation you have in mind. It would be trivial to
add however, if all you're looking for is an option to the
"measure minmax" command that would pad the bounding box with
the per-atom VdW radii. If that's all you're asking for, let me know
and I'll see about adding it in the next beta version.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 15, 2007 at 06:27:53PM -0300, Cesar Luis Avila wrote:
> When using
> measure minmax [atomselect top "index 0"]
> it returns the coordinates of the atom's center, ie {0 0 0} {0 0 0}
> Is there a way to calculate minmax including the atom's VdW volume? I
> mean in a way that for a 1 A radius atom it would reply something like
> {-1 -1 -1} {1 1 1}
> I would say that I am not interested in asking one atom's volume, but I
> would like to know the volume of a whole molecule.
>
> Regards
> Cesar 

-- 
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