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

massimo sandal devicerandom at gmail.com
Thu Mar 19 09:20:57 PDT 2015

Hi all,

Sorry for my late reply and many thanks, your comments really helped.
Elaine Meng, your links really helped a lot. Two things:

1) I actually re-checked my dataset and it seems I have no negative SAS
-only negative SES values sometimes.
2) Can someone confirm the SAS values are in units of angstrom squared?


2015-03-11 23:18 GMT+01:00 Tom Goddard <goddard at sonic.net>:

> 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).
>         Tom
> > 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
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
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