Hi Cedric, When a molecular surface is calculated (the first time it is shown), the solvent-excluded and solvent-accessible areas are also calculated. The overall totals and total per disconnected part ("component") are reported in the Reply Log. At the same time, it creates atom and residue attributes named areaSES and areaSAS. Chimera only shows the solvent-excluded surface, but areas for both types of surfaces are computed: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces

So after you show a surface, you can use these atomic or residue attributes in various ways. To see a histogram of the values, start Render/Select by Attribute (under Tools... Structure Analysis, among other places). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#...

With this tool, you could color by the values, or select only atoms (or residues) with values in a certain range, or write out the values for all atoms or just the selected atoms to a text file with "File... Save Attributes". The values can also be used in command-line specifications, and you can show them as labels. Example commands: open 1zik surf color green @/areaSAS>40 ~surf labelopt info areaSAS la @n You can get totals over selected atoms using Attribute Calculator (under Tools... Structure Analysis). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculat...

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 Apr 21, 2009, at 6:23 AM, Cédric Govaerts wrote:

Hi there, I want to compute accessible surface area for the backbone, as I want to compare the predicted amide deuteration between two conformations of a protein (I have PDBs for both). I tried with VADAR but the results are puzzling, I suspect they are not correct (the more open structure gets a lower score).

Is there a way I can do something like that in Chimera ?

In other word I need to compute how exposed to the solvent are the backbone atoms (in fact just the NH) and get a table for every position. Cannot seem to find a simple way to do that with Chimera...

Thanks again for your help Cedric