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

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 30 15:15:40 PST 2009

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:


To use "measure" you need a recent daily build (it isn't in the Dec  
2008 production release).
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

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

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