[Chimera-users] Residue exposition cutoff

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 5 09:22:37 PDT 2010

Hi Yasser,
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?
> Thanks,
> best regards

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