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: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003291.html
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003597.html
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: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/003995.html> 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 GetArea: <http://curie.utmb.edu/getarea.html> I hope this helps, Elaine ----- 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