VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Fri Jun 18 2010 - 14:15:10 CDT

Thanks very much, that is useful information: area/point = (surface area of
the atom)/(number of randomly sampled points).

the surface are of the 'atom' is actually the area of the sphere with a
radius = (atom radius + probe radius), right?

It looks from the code that 500 random points are used...is that correct?

So...*IF* I could assume that every atom considered in the SASA calculation
has the same radius, I would know the area/point, and I could easily
calculate the area for each separate patch.

one last question: are the H's and the C's considered seperately for the
purpose of the SASA calc? or do you just puff out the radius of the carbons
a little bit and save some calculation time?

Thanks very much for the help.
Ed

On Fri, Jun 18, 2010 at 12:10 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>