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.

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@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@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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