[Chimera-users] calculate buried surface area

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 5 09:12:41 PST 2013


Hi Bala,
I can't think of any (noncoding) way in Chimera for looking at surfaces geometrically and getting the area of the monomer 2 molecular surface that is inside the ESP isosurface from monomer 1.  However, it sounds like it just boils down to getting the surface area of monomer 2 at which the ESP from monomer 1 is above (or below) some value.  In that case, you could color the monomer 2 molecular surface by the ESP from monomer 1 and then use the script that was posted yesterday to get surface area based on color.
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-December/009401.html>

Since in this case you want the coloring to reflect the ESP right at the surface instead of 1.4 angstroms outward, when coloring be sure to turn OFF the option for "Surface offset" in Electrostatic Surface Coloring. 
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 5, 2013, at 7:58 AM, Bala subramanian <bala.biophysics at gmail.com> wrote:

> Friends,
> 
> I have a dimer protein (say monomers 1,2). I have calculated the electrostatic potential of monomer 1 using apbs. I used volume viewer to display the electrostatic surface. 
> 
> I see that the elect. surface of one monomer 1, touches the vdw surface of monomer 2 at a contour level of 1. I want to calculate the total surface area of monomer 2 that is exposed/buried within the elec. surface of monomer 1. Is there any simple. If not suggestion how i can do it with a python script perhaps.
> 
> Thanks,
> Bala




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