[Chimera-users] residue.areaSES returns 0 for buried residues

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 15 13:22:59 PDT 2017


Hi Kevin,
I think you are misunderstanding the the SES… it is not the complement of the SAS; the distinction is whether it is the surface traced out by the surface of the probe (SES) or the center of the probe (SAS) rolled over the structure of interest.  SES is like a smoothed VDW surface of the molecule, since the crannies where the probe doesn’t fit are removed. Both SAS and SES will be zero for completely buried residues. 

I’m sure there are some good images showing the two types of surface, but I don’t have one handy at the moment.

We have instructions for calculating the relative exposure of amino acid residues.  It uses the SES of a residue in the structure of interest normalized by the SES of that same type of residue in an extended Gly-X-Gly tripeptide, as a proxy for the unfolded state:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html>

If I remember correctly, the procedure gives fractional values, but they could be multiplied by 100 to give %.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 15, 2017, at 9:50 AM, Kevin Jude <kjude at stanford.edu> wrote:
> 
> Hi Chimerans-
> I am trying to use Chimera to list percent accessible surface area by residue for a structure by calculating (solvent accessible area SAS) / (solvent excluded area, SES). For some reason, for residues that are completely buried, Chimera returns not only SAS=0, but also SES=0, and thus those residues aren't included in the percent accessible calculation. Does anyone have a clue for this behavior?
> 




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