VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 06 2013 - 10:37:51 CST

Hi,
  Use an atom selection for the sites of interest instead of the default
selection of "all". If you're not familiar with VMD atom selections yet,
I would recommend that you work through the VMD tutorials.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Nov 06, 2013 at 07:01:15PM +0330, Marzieh Dehghan wrote:
>
> Dear users,
>
> 1- after protein-protein docking , I want to use ramachandran plot to
> know the amount of secondary structures in the interaction sites, how to
> use ramachandran plot that just shows all secondary structures in the
> interaction sites not all molecules.
>
> thanks in advance 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/