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

Tom Goddard goddard at sonic.net
Wed Mar 11 15:18:28 PDT 2015

Hi Massimo,

  I think buried solvent accessible area (SAS) is most often used when buried areas are reported.  Negative values of buried SAS are impossible, that would be a bug, probably a failure of the surface calculation, and if you see a case of that could you send me a Chimera session that demostrates it?  Unfortunately with erratic surface calculation (which does not always report when it goes awry) you cannot be certain the numbers are correct.  I think buried SES can give a negative value in weird cases because the toroidal surface patches created by the probe sphere rolling between the two sets of atoms could be large (e.g. the buried area between two spheres whose surfaces are separate by a bit less than the probe radius).


> On Mar 11, 2015, at 5:24 AM, ms <devicerandom at gmail.com> wrote:
> 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
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