Hi Thiru, As soon as you show a surface (command "surface" or "Actions... Surface... show" in the menu), residue surface area values are automatically stored as attributes named areaSES (solvent-excluded surface area) and areaSAS (solvent-accessible surface area). The surface you see is the solvent-excluded surface. The values will still be there even if you hide the surface later. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ representation.html#surfaces> You could select all the residues with surface areas greater than zero (or some small value) and then write a PDB file containing only the selected residues. How to select: You could do it with a command; for example, to select all residues with solvent-accessible surface area greater than 10 A**2: select :/areaSAS>10 Or you could use a graphical interface that shows a histogram of the values: Choose "Select... By Attribute Value" from the menu, then show attributes of "residues" and choose the attribute "areaSES" or "areaSAS" as desired. Move the vertical bars to enclose the range of values you want to select, click OK. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#select> How to write the PDB: Choose "File... Save PDB" from the menu and make sure to turn on the option "Save selected atoms only". The same thing could also be done using the command "write" with its "selected" option. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> Note that the surface areas will include any pockets inside the protein. If you don't want the surfaces of those interior bubbles or pockets to be included, there is an additional step before selecting the residues: Ctrl-click on the surface to select it, choose "Actions... Inspect" from the menu; in that dialog, Inspect "MSMS Surface" and change "show disjoint surfaces" to "false." <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ inspection.html#msmsprop> 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 Nov 22, 2008, at 12:16 PM, Thiruvarangan Ramaraj wrote:
I am using Chimera molecular viewer, to identify the surface residues and then write all the identfied residues on the surface to a file in a pdb format. Any help would be greatly appreciated. Thank You Thiru