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#...

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#pa...

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@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