Dear Dr.Elaine Meng, Thanks a lot for your kind advise. It really helped me a lot. Regards, Soumya Elaine Meng wrote ..
Dear Soumya, When you show a surface, the surface area values are automatically assigned to atoms and residues. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces
You can select resides with surface area greater than some value, which will be the residues at the surface. The residues with small or zero surface area will be the ones buried on the inside.
For example,
open a structure (I opened PDB 2gbp as an example) use menu "Actions... Surface... show" then you can hide the surface, "Actions... Surface... hide" then to select by surface area value, choose "Select... by Attribute Value" in that dialog: change from attributes of "atoms" to "residues" if you want to select whole residues choose Attribute: "areaSAS" (if you want solvent-accessible surface area) or "areaSES" (if you want solvent-excluded surface area) move the vertical green bars to enclose the values of interest, click Apply It is the solvent-excluded surface that is displayed in Chimera. For example, I chose residues with areaSES values >30 (one green bar near 30, the other near the maximum value). You could use a different cutoff, but probably it should be bigger than zero. That generally selects the residues on the surface, and now you can use the Actions menu to do something else to those residues (color them, label them, write list of residues to a file, etc.)
Instead of a dialog you could also select them with a command, e.g.
select :/areaSES>30
One thing to think about is that usually there are surface bubbles on the inside, and some of the residues may have surface area from these bubbles and not the real outer surface of the protein. You can change the surface to not include these inside bubbles:
open Model Panel (menu "Favorites... Model Panel") in that dialog: choose the MSMS surface model in the left side click "attributes" button on the right side in that, change "show disjoint surfaces" to "false" Close dialog now choose "Select... by Attribute Value" again in that dialog: Refresh... Values and proceed as above to choose residues by surface area value (or again, you could use the command instead)
Here is a previous answer to a similar question: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003291.html
I hope this helps, Elaine
On May 14, 2009, at 5:46 AM, Soumya Ghosh (Systembiologie) wrote:
Dear Dr. Elaine C. Meng, Thanks a lot for your kind help. It really worked nicely.Can I afford to have some more questions. When I put my protein in the CHIMERA, I get the 3D module of it and it exhibits the α- helices and the ß-sheets very nicely. Now if I want to highlight the aminoacids that are specifically on the surface of the N -terminal or the amino acids that specifically embedded in the core, is there any provision to that. I tried with the Action; surface; show. With these commands it is visible that a structure appears that cover sometime the loops/helices/sheets fully or partially. Now my problem is, that is the sructure which is visible is it the surface? The amino acids which are highlighted are also from the surface? Can you kindly help me in this regard.
Thanks with regards,
Soumya