VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 21 2010 - 23:43:32 CST

You can use spatial criteria to create atom selections and then
query the number of atoms in the resulting selection. As for the
possibility of double counting atoms, perhaps due to slight overlap
in your spatial selection critera or for some other reason, you could
presumably determine if any double-counting has occured by using a third
"and" selection, constructed from both of the other selections, and seeing
if you get any atoms that are in both of the subunit selections you create.
You could then subtract off any results that somehow manage to get double
counted. You can get the number of atoms in a selection using "$sel num".

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 21, 2010 at 06:09:10PM -0500, Naiyin Yu wrote:
> Hello,
>
> I have a question about count the number of atoms, ie waters in a
> certain volume, which is constructed by couples of subunits and I
> already known the boundary of the edges of each units. I was wondering
> whether VMD could count the number of atoms inside the subunits. And is
> there any criteria to the min of the subunits (ie larger than the size
> of the atoms volume) so I could avoid double count.
>
> Thanks a lot!
>
> Naiyin 

-- 
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