[Chimera-users] Electrostatic Potential

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 12 08:02:04 PDT 2019

Hi Fernando,
An important thing to understand is that the color is changed gradually from red to white, and gradually from white to blue.  So there is a lot of surface coloring that is “between” red and white, and between white and blue.  Only the surface points with values   -10 or lower are actually red, and those with 10 or higher are actually blue.  It is unclear exactly what quantity you want to measure.

There is no simple feature like a command to do it. You would have to use python scripting, but somebody else would have to advise on any details of that.  Also, first think carefully about what you really want to measure.  

This electrostatic surface coloring is really meant for visualization, comparison “by eye.”  For quantitative analyses, maybe the two websites I mentioned earlier would be better tools.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 11, 2019, at 7:27 PM, Fernando Villa <fer.vdl1928 at gmail.com> wrote:
> Dear all Chimera users
> In UCSF ChimeraX version 0.91 (2019-08-30)
> I opened a .pqr file (generated with pdb2pqr in Chimera 1.14)  and then I opened a .dx file (generated with APBS in Chimera 1.14)
> Then I input the commands:
> >surface
> >color electrostatic #1 map #2 palette -10,red:0,white:10,blue
> <image.png>
> Is it possible to calculate the red and blue area in Å2 of the molecule?
> Best regards,
> Fernando

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