[Chimera-users] Calc buried surface area between 2 chains

[Elaine Meng]

Hi Tom,
Happily there is a command to do it, but first I'll explain your  
current results:

Even though you are summing over a certain set of atoms, the surface  
does not necessarily enclose that set.  If you have a single surface  
enclosing both A and B, any sums will not include the part buried  
between A and B.  Thus it makes complete sense that the surface area  
of A alone, with surface enclosing A only, is larger than the surface  
area of A in the AB combined surface, because B buries part of A.

You could tell Chimera to make separate surfaces for A and B and sum  
the areas in those.  However, if it is really the buried surface area  
you care about, use the new "measure buriedarea" command -- it  
calculates the combined and individual surfaces (without creating  
displays) and takes the difference.  More details on this command and  
how to use it:

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html>

To use "measure" you need a recent daily build (it isn't in the Dec  
2008 production release).
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                       http://www.cgl.ucsf.edu/home/meng/index.html

On Jan 30, 2009, at 2:49 PM, Tom Duncan wrote:

> I saw an earlier post (Dec. 29, 2008; Digest vol. 68, issue 28) in
> which Elaine Meng described a procedure for calculating surface area
> for selected atoms. I did this for atoms on chain A that were selected
> as contacting atoms on neighboring chain B, but the sum(atom.areaSES)
> probably includes area buried within the chain A, not just between the
> 2 chains.
> I tried checking this by calculating the sum(atom.areaSES) for chain A
> (all atoms in A) in the whole model, then again for a model from which
> chain B was deleted before calculating the surface. However, the
> results indicated a larger areaSES for chain A in the absence of chain
> B!
> There were some errors reported in calculating the surfaces; perhaps
> this contributed.
>
> Is there a better way to calculate the buried surface on 1 chain due
> to contacts with a 2nd chain?
>
> Thanks,
> Tom Duncan
>