[Chimera-users] Electrostatic Potential

[Fernando Villa]

an apology, don't attach the file correctly, here it goes, regards


ATTE
Fernando Villa Díaz



El lun., 16 de sep. de 2019 a la(s) 15:20, Fernando Villa (
fer.vdl1928 at gmail.com) escribió:

> 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: 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
>>
>>
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription:
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190916/7275fe0d/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 306082 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190916/7275fe0d/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Test_MEP_Protein.xlsx
Type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
Size: 1561781 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190916/7275fe0d/attachment.xlsx>