# [Chimera-users] Electrostatic Potential

Tom Goddard goddard at sonic.net
Mon Sep 16 15:39:04 PDT 2019

```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 <fer.vdl1928 at gmail.com> 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.
> <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 <mailto: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 <mailto: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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> <Test_MEP_Protein.xlsx>_______________________________________________
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