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

Tom Duncan duncant at upstate.edu
Fri Jan 30 14:49:28 PST 2009

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  
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?


Tom Duncan

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