[Chimera-users] polar and nonpolar surface area

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 23 09:54:41 PDT 2019

Dear Susanna,
This sounds like the same question others have been asking recently… maybe a class assignment.  If so, you can tell the others in the class so that they don’t have to ask here again!  :-)

Please see this recent response, and links therein:

…including the following, which has with more details starting at the fifth paragraph, “However, you can get the total surface area given some range of hydrophobicity values…”

…or a web server you could try instead of Chimera:

These answers suggest selecting polar and nonpolar residues, giving a few different options for deciding which ones are polar and nonpolar, and then just adding up the surface area from the selection.  Maybe by “customize” you meant deciding for yourself which is polar and nonpolar?  You can just select a list of whatever residue types you want, e.g. command:  select :asp,glu,his,lys,arg

You don’t have to worry about selecting only the atoms on the surface, because if they are not on the surface they will just add zero area to the total and the result will be the same.  Selecting a residue selects all the atoms in that residue.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 21, 2019, at 3:12 PM, Susy López <susannalopez18 at gmail.com> wrote:
> Dear all
> I am starting to use Chimera as a master's student and I have some difficulties.
> I know how to select the amino acids that are part of the surface of my protein. However, I don't know how to select the atoms of the surface. Specifically, the atoms accessible to the solvent.
> My second question is:
> I would like to know how polar amino acids (arginine, asparagine, aspartic acid, cysteine, etc.) and non-polar amino acids (alanine, glycine, isoleucine, leucine, etc.) can appear. Is there any configuration that allows me to identify polar and non-polar amino acids for edit them? Is it possible to customize those amino acids when I select them?
> I would be grateful if someone could help me, thank you.
> Best regards,
> Susanna

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