VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 18 2010 - 13:10:08 CDT

Hi,
  The -samples flag controls how many random sample points are used
to estimate the surface area for each atom. The points are distributed
randomly over the sphere, and the area is estimated by multiplying the
fraction of samples that are exposed by the surface area of the sphere
for the atom under consideration. When you retrieve the actual list of
sample points, you are getting the points that passed the solvent
accessibility test for the combination of selection and/or restricted
selection you provided. Does that answer your question?

You can see the source code that implements the calculation in the
measure_sasa() routine here:
  http://www.ks.uiuc.edu/Research/vmd/doxygen/Measure_8C-source.html#l01058

(that URL will change with time, but it's good for the short-term)

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 17, 2010 at 10:47:34AM -0600, Edward Lyman wrote:
> Hi all,
>
> I am looking for an explanation of the -samples flag for measure sasa
> (somehow it has been omitted from the manual). I guess it is simply the
> density of points that is used to sample the surface, but I would like to
> know what is the default value, and what the value means. For instance,
> does each point represent a (roughly) constant area? Or is each point a
> vertex in a more complicated (eg, Delaunay) triangulation, and so could
> represent a wide range of areas?
>
> My interest stems from the following problem: I have used "measure sasa"
> to identify several distinct patches of solvent accessible residues on the
> surface of a protein. I can store those points, and then post process them
> using a simple (breadth-first) search algorithm to automate the process of
> distinguishing different patches. Now I want to know the area of each
> patch. If each vertex represents a constant area...problem solved. But if
> the surface is more complicated...the problem becomes considerably
> trickier, and I then have to recover the (nonoverlapping) triangles in
> each patch and add up their areas.
>
> Thx,
> 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