VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 25 2010 - 17:00:31 CST

Hi,
  Sorry for being slow to reply, I've been swamped finishing papers
and getting some new code up and running...

For 1) you would feed the list of points into 'draw' commands to
draw them however you like.

For 2) yes, the -restrict command can be used to prevent part of the
structure from contributing. You can visualize the points to help
you figure that out.

Let us know if you need more help.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 17, 2010 at 01:40:53PM -0700, Edward Lyman wrote:
> Hi all,
>
> 2 questions about vmd's built in sasa calculator:
>
> (1) how do i visualize the surface data after i store it using the -points
> option?
> (2) will the following command measure for me the sasa for $subsel,
> excluding the surface area of $subsel that is occluded by $sel?
>
> measure sasa [atomselect top "$sel"] -restrict [atomselect top "$subsel"]
>
> Thanks!
> Ed 

-- 
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