VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Thu Jun 17 2010 - 11:47:34 CDT

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