Re: [Chimera-users] Electrostatic Potential

Hi Fernando, I don't understand what you need vertex coordinates for. But you could put a print statement into the Chimera Python code that does surface coloring to output vertex coordinates and potential values. This would be in file chimera/share/SurfaceColor/__init__.py or on Mac in Chimera.app/Contents/Resources/share/SurfaceColor/__init__.py in the volume_values() routine change def volume_values(self, surface_piece): p = surface_piece xf = p.model.openState.xform v = p.geometry[0] n = p.normals return self.offset_values(v, n, xf) to def volume_values(self, surface_piece): p = surface_piece xf = p.model.openState.xform v = p.geometry[0] n = p.normals values, outside = self.offset_values(v, n, xf) print '\n'.join('%.5g %.5g %.5g %.5g' % (x, y, z, val) for (x,y,z), val in zip(v, values)) return values, outside Use the Surface Color tool and the vertices and values will be printed to the reply log. Tom

On Sep 16, 2019, at 1:20 PM, Fernando Villa wrote:

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 mailto: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 mailto: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

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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