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

Kevin Jude kjude at stanford.edu
Fri Sep 15 15:08:49 PDT 2017


Elaine -
Thanks, this is very helpful. I remember, now, calculating SES with GRASP
years ago, but it's been a while, so I'd gotten my definitions confused.

Best wishes
Kevin

--
Kevin Jude, PhD
Research Specialist in Structural Biology, Garcia Lab
Departments of Molecular & Cellular Physiology and Structural Biology
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431

On Fri, Sep 15, 2017 at 1:22 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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