[Chimera-users] nonpolar and polar surface area

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 16 12:57:53 PDT 2019

Hi Bailey,
You will have to decide for yourself which residues you want to consider as polar and nonpolar.  Then after you show the surface of the protein, you can select any subset of the residues (or atoms) and then sum the surface area from that subset using the Attribute Calculator tool.

This is described in more detail in this recent post.  Skip down to the fourth paragraph, starting "However, you can get the total surface area given some range of hydrophobicity values…”

Alternatively, you could take a look at the GetArea web server mentioned in this follow-up:

(I changed the subject line of the message to something more descriptive to help others find it later.)
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 16, 2019, at 12:23 PM, Bailey Onken <onken031 at umn.edu> wrote:
> Hello,
> I am currently a student in Biochemistry. I have a protein and I am trying to separate polar and nonpolar residues located on the surface of these molecules and then finding the values for the surface area associated with polar and nonpolar areas. If you can help me get to this function I would be very grateful. 
> Thank you very much, 
> Bailey 

More information about the Chimera-users mailing list