[Chimera-users] Electrostatic Potential

[Fernando Villa]

Hi all Chimera users,



I would like to know how to calculate the values of Coulombic ESP on the
interface between two proteins:



At the moment I have done the following:

*UCSF Chimera version 1.14

Commands:

    open <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html>
 1avx

display

~longbond
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/longbond.html>

split <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>

delete <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html>
 solvent

surf #0.1



Tools>Surface/Binding analysis>Coulombic surface coloring

>Check the box compute grid

>Apply

>Surface color>Options

                     >Check the box Report value at mouse position

                     >Click color:



All the electrostatic potential values appear by Coulombic Kcal/(Mol.e) at
the mouse position:


[image: imagen.png]

Commands:

~surface #0.1

measure buriedArea  #0.1  #0.2

select #0.1@/buriedSASArea> 1

surf sel



Volume viewer>Tools>Values at atom position>Click Histogram


[image: imagen.png]


Is there a way to save all the ESP Coulombic values in the selected
interface surface in a file?

Is it possible to calculate the polar and non-polar surface area in the
interface?

Regards,

Fer.





El lun., 16 de sep. de 2019 a la(s) 17:39, Tom Goddard (goddard at sonic.net)
escribió:

> 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)
> 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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>>
>> <Test_MEP_Protein.xlsx>_______________________________________________
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