[Chimera-users] Residue Accessibility

[Elaine Meng]

Hi Luis,
The previous post is mostly accurate except for the URL of the Getarea  
server, but now there is an additional easier way to get the surface  
areas of residues in Chimera:  As soon as you show a surface, each  
residue's solvent-accessible and solvent-excluded surface areas are  
available as the residue attributes areaSAS and areaSES, respectively:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces 
 >

In Render by Attribute (under Tools... Depiction) you can see  
histograms of these residue attributes, or write them out to a file,  
color structures to show the values, etc.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render 
 >

However, these are raw surface areas, not normalized by any fully  
exposed state.  Other than somehow obtaining those fully exposed  
surface area values for each residue type, assigning them as  
attributes with Define Attribute, and then using Attribute Calculator  
to generate a new, normalized attribute, you could use the Getarea  
server as previously described.  As far as I know it still provides  
the "Ratio (%)" relative accessibility value, and its newer URL is
<http://curie.utmb.edu/getarea.html>

The Attributes tutorial part 2 includes using the atom attributes  
areaSAS and areaSES in Attribute Calculator to create a new atom  
attribute named "convexity"; residue attributes would be handled  
analogously.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html#part2 
 >

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Oct 21, 2008, at 10:14 AM, Luis Alberto Alvarez wrote:

> Hello,
> I am trying to calculate the relative surface accessibility of  
> residues (It will come to getting the solvent accessibility I guess)  
> and the only information I found is from a post in the mailing list  
> dating to 2005 (http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-October/000482.html 
> )
> I am just wondering if there is anything new in this front or I  
> should just follow the 2005 instructions.
> Thank you