[Chimera-users] Electrostatic Potential

[Elaine Meng]

Hi Fernando,
You already calculated the values of Coulombic ESP on the interface: it is displayed.   However, I guess you mean that you want to write the values that you have already shown with coloring to some file.  There is a “surfval.py” python script in the Chimera scripts page that is supposed to do that, although it may be the whole surface (not just the interface), see:
<http://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts>

The Coulombic Surface Coloring tool (and command) also has an option to open the grid of Coulombic ESP values as as separate model.  This grid is what is interpolated to get the values for surface coloring.  This separate grid model can be saved using the Volume Viewer tool’s File menu.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html#volume>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html>

Getting polar/nonpolar surface area is the same question you asked in September.  Here were the responses:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016139.html>
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016159.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 30, 2019, at 9:35 AM, Fernando Villa <fer.vdl1928 at gmail.com> wrote:
> 
> 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 1avx
> display
> ~longbond 
> split
> delete 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:
>  
> <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
> 
>  
> <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
>>>