[Chimera-users] Electrostatic Potential

[Fernando Villa]

Dear Tom and Chimera users,

In ChimeraX or Chimera, is it possible to calculate the number of vertices
and their respective total charges?

I calculated the electrostatic potential surface (Coulombic) with another
program, it gave me the following results (attached in this email) and I
calculated the area in red and blue, above and below a threshold = 0.

Unfortunately, these results do not help me, because I need to obtain an
electrostatics calculations from Adaptive Poisson-Boltzmann Solver
(Calculations that I have already made for study proteins with PDB2PQR and
APBS, in interface with Chimera: .pqr and .dx files and emulated in Chimera
X)

e.g.
[image: image.png]

Now my question is:
Can I obtain these results of vertices and charges in a file from Chimera
or Chimera X (possibly .cvs, .txt, etc.), so that I can make the
corresponding calculations?

I would greatly appreciate your help

best regards,

Fer



El lun., 16 de sep. de 2019 a la(s) 13:03, Tom Goddard (goddard at sonic.net)
escribió:

> Hi Fernando,
>
>   Instead of thinking about the coloring, it would be clearer to ask how
> much surface area has electrostatic potential value >= 5.  Chimera does not
> have any code to compute that, although it is something we could add to
> ChimeraX.
>
> Tom
>
>
> 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
>
>
> ATTE
> Fernando Villa Díaz
>
>
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