[Chimera-users] electrostatic surface

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 13 09:13:51 PST 2017

Hi Jiri,
If I understood correctly, you either 
(1) calculate ESP map separately for each chain and only show its own ESP on its surface
(2) calculate one ESP map for the whole protein (all chains) but show the values on separate chain surfaces

It really depends on what you want to show.  in the second one, charges from each chain affect the values/coloring of other chains.

My guess (others may disagree) is that it is more traditional to color a surface from the ESP calculated using only the atoms inside the surface.  So if you are showing separate surfaces for the chains, that would be calculating ESP separately for each one (#1 above).  However, it could also be that you calculate only one ESP map and show only one surface for all the chains combined instead of separate surfaces (not splitting, maybe that is choice #3).  Still, I don’t think #2 is wrong either… you should just say in the figure legend what you did.

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

> On Feb 13, 2017, at 5:32 AM, chemocev marker <jirivitali at gmail.com> wrote:
> Hi
> I am calculating the electrostatic surface of the protein that has a peptide bound inside the catalytic camber. There are two ways to calculate, either i can split the molecule in indivual chain and calculate their surface indivdually and run the APBS server for the electrostatic potential, or i can do it use the surfcat command. Both of them works but the results are different. To me the results are more logical by splitting the molecule in indivual chain, but u am not sure if its right to do that specially when you want to measure the electrostatic potential. What is your opinion.
> best
> Jiri 

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