[Chimera-users] Residue exposition cutoff
meng at cgl.ucsf.edu
Mon Apr 5 09:22:37 PDT 2010
Actually you don't have to use DMS ... if you show a surface in
Chimera it also automatically computes the SES (solvent-excluded
surface) and SAS area per atom and per residue, attributes named
areaSES and areaSAS. For more details, see these previous posts:
Some notes about areaSES and areaSAS:
(1) if you don't want to include inside bubbles in the surface area
calculations, after creating the surface(s) remove the inside bubbles
with the command: setattr s allComponents false
(2) the surface that Chimera displays is the SES (also known as
Connolly surface or molecular surface), not the SAS, although both
sets of areas are calculated
Actually Tom Goddard mentioned the areaSAS attribute briefly in an
earlier reply to you:
As to what cutoff should be used for classifying atoms or residues as
buried or exposed, I'm not aware of any commonly used value. It is a
more philosophical issue that depends on your ultimate purpose. You
might try coloring by different cutoffs to try to decide what is
appropriate for your research (keeping in mind that the SES is what
Chimera actually displays), or read publications of similar work to
see what other researchers have used. In publications, I have seen
residues classified by "fraction" or % of the surface area of a
residue in the structure divided by the area of that same type of
residue in a hypothetical fully exposed state, but I don't remember
the exact cutoffs used, and Chimera does not provide the fully exposed
values. An example of a program that does provide such values is
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Apr 3, 2010, at 1:38 PM, Yasser Almeida Hernández wrote:
> Hi all....
> I have 2 question, beyond Chimera's issues.
> 1 - There is some cutoff value to consider a residue or more
> strictly, an atom exposed to the solvent?.
> 2 - Could i set a this cutoff using the area values and types (SR0,
> SC0 and SS0) from the DMS program output?
> 3 - Wich program you recommend to compute SAS?
> best regards
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