[Chimera-users] Electrostatic Potential

[Fernando Villa]

Thank you very much Dr. Elaine and the Chimera work group, now I have a
better picture of what I have to do.

Thank you for guiding me in this part,

I appreciate it

Best regards,

Fer


ATTE
Fernando Villa Díaz



El jue., 12 de sep. de 2019 a la(s) 10:02, Elaine Meng (meng at cgl.ucsf.edu)
escribió:

> 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
> -----
> 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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