Dear PK, This can be done fairly easily by the following:

(1) delete any solvent, ions, ligands that you don't want to consider in the surface calculation

(2) run Surface Area/Volume (in the Surface/Binding Analysis section of the Tools menu) to compute the "Accessible Surface (Gerstein)" and name the resulting attribute "accessibleSurface" - I believe these are the default settings. This sends coordinates of all remaining atoms to the StrucTools server. A warning message will appear if the server is unable to figure out the proper radii to use for any atoms. Here is the man page for the Surface Area/Volume tool: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html

(3) select all atoms with surface areas > 0 (or some other small cutoff), for example with the command: sel @/accessibleSurface>0

(4) write out the coordinates of the selected set of atoms (Actions... Write PDB)

The set of exposed atoms may differ slightly from the ones you can see at the surface in Chimera because the server uses radii that are slightly different than the ones in Chimera. We plan to have Chimera's own surface calculation report surface areas in the future, which would allow you to see the results of changing radii and other parameters in Chimera. For now, however, just the values from the StrucTools server are available. An alternative to (2) above is to use a different method from the same server, "Surface Area (MSMS)" instead of the Gerstein method mentioned above, and then select on values of the attribute msmsArea_SAS (if you want the solvent-accessible surface) or msmsArea_MS (if you want the molecular surface, aka the solvent-excluded surface). Again, you cannot control the parameters such as radii used by the server.

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

On Feb 28, 2006, at 3:19 PM, kovzany@go.com wrote:

Dear All,

Is there an easy way to select and save set of atoms (with their names and coordinates) representing VdW or solvent accessible surface of the given molecule?

thanks,

PK _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users