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@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