[Chimera-users] Electrostatic potential surface area

Yasser Almeida Hernández yasser.almeida at gmail.com
Wed Apr 13 05:53:28 PDT 2016


Thanks for your reply! with a few modifications, I think I can do what I
want.

On the other hand, it would be great that in futures developments of
Chimera, create a mouse selection tool for surfaces patches, something like
a "magic wound" like graphical packages like Photoshop or Gimp. In
principle the idea would be select a surface according to a threshold value
(ej. electrostatic potential) set by the user. With this, several
selections could be created/added/subtracted, calculating the surface area
and the ratio respect with the total area.

Regards

Yasser

2016-04-12 18:53 GMT+02:00 Elaine Meng <meng at cgl.ucsf.edu>:

> 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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160413/e20ba82e/attachment-0001.html>


More information about the Chimera-users mailing list