[Chimera-users] Electrostatic potential surface area

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 12 09:53:13 PDT 2016


Note that this script gets the area of the patches that are more red than blue, which is traditionally the part with negative potential.  You could either subtract from the total area to get the positive-potential area, or do the coloring the opposite of the conventional way.

Elaine

> On Apr 12, 2016, at 9:45 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Yasser,
> I believe Tom Goddard wrote a python script to do this a couple years ago…  it is described in this previous post, with link for getting the script:
> 
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-December/009401.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 Apr 12, 2016, at 1:25 AM, Yasser Almeida Hernández <yasser.almeida at gmail.com> wrote:
>> 
>> Hi all,
>> I did some calculations of the electrostatic potential using APBS and Delphi. I want to calculate the surface area of a positive patch in my protein.
>> There is a way to select and compute the surface area/patch, filtering by the electrostatic surface value?
>> Thanks in advance
>> Yasser




More information about the Chimera-users mailing list