VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 01 2006 - 16:44:04 CST

Hi,
  So you're looking for a script to identify "buried" atoms, or
waters in internal cavities? Finding buried protein atoms might
be doable by selecting atoms with near-zero SASA values, the inverse
of what someone else just asked for. Finding buried waters would
require some trickery, perhaps you could calculate the SASA values
for waters within a cutoff of "protein", and then sift through those
finding atoms with near-zero SASA values. That may or may not work,
but it's an idea to start with.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 01, 2006 at 12:50:00AM +0000, ziemys_at_ecr6.ohio-state.edu wrote:
> Hi,
>
> How to select atoms (e.g. water molecules) inside protein (within protein volume) ?
>
> With best
> Arturas
> 

-- 
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