[Chimera-users] Interaction interface between two residues and measure buriedArea

[ms]

Dear all,

I am trying to understand what is the area buried between two residues 
(or between one residue and two other ones) in several structures. It 
seemed to me the best way to do this was to use the command "measure 
buriedArea :res1 :res2" on the full structure (once all non-protein 
components have been cleaned out of it). The overall trend of these 
measures seems consistent with visual inspection.

However I have a couple of questions about it:

1) I am unsure about what value is best to use/compare, buriedSAS and 
buriedSES. It seems to me that the difference between the two is 
essentially in the geometrical protocol used. Is there any general 
wisdom about what do they physically mean and how should I approach each 
value?

2) In some cases I receive *negative* values for buriedSAS and/or 
buriedSES. Looking on the ML it seems that it is a symptom of a buggy or 
failed area calculation (e.g. 
http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005119.html 
). However it also says that I should see a "fallback" warning on the 
Reply Log -I see nothing of the sort. How do I troubleshoot this? Also 
in cases where the calculated value is positive, how can I be sure that 
the values are indeed meaningful?

Any other feedback on the kind of measurement I am trying to do is more 
than welcome.

Thanks a lot,
Massimo