[chimerax-users] Question about Coulombic electrostatic potential

[Sunisa Yoodee]

Dear All,

Thank you so much for your suggestion.

Best Regards,
Sunisa Yoodee

ในวันที่ จ. 21 ก.พ. 2022 เวลา 01:00 Elaine Meng <meng at cgl.ucsf.edu>
เขียนว่า:

> Dear Sunisa,
> There is no single value for a protein - the electrostatic potential is a
> quantity that varies in 3D space, so instead of one value it is many
> different values on a 3D grid.
>
> Getting to Jacob's question of how to save values:
>
> ChimeraX does not yet have the option to generate a map model from the
> Coulombic electrostatic potential calculation.  To do that, you would need
> to use Chimera instead.  Chimera's "coulombic" command, see the last 3
> options on this page:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html>
>
> ... or the GUI, Chimera menu: Tools... Structure Analysis.... Coulombic
> Surface Coloring, the "Compute grid..." options:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html
> >
>
> Then in Chimera, you could save that map model to a file with the "volume"
> command, see saving options:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output
> >
>
> Formats are MRC, NetCDF, BRIX, IMAGIC, or Chimera map format.  I don't
> know if they are meant to be  human-readable, you would need to investigate
> that further yourself.
>
> Alternatively if you just mean you want to know the value of the potential
> at some specific point(s) on the protein surface, see this recent post:
> <
> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003337.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 Feb 19, 2022, at 6:05 AM, Anderson, Jacob via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > To piggy back on this question of getting more quantitative information
> out of ChimeraX's electrostatic/coloumbic functions, is there a way to save
> information about the electrostatic surface as a readable text file (or a
> .dx file (if that one is human readable))?  I was hoping to quantitatively
> get a delta electrostatic surface of two surfaces at different propka-ph
> values.
> >
> > Or perhaps a way to generate that difference surface in ChimeraX?
> > From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of
> Sunisa Yoodee via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
> > Sent: Saturday, February 19, 2022 12:22 AM
> > To: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> > Subject: [chimerax-users] Question about Coulombic electrostatic
> potential
> >
> > Dear UCSF ChimeraX
> >
> > We used the ChimeraX program to calculate electrostatic potential. By
> using the coulombic command, a molecular surface was generated and colored.
> However, we also need the electrostatic potential value (kcal/(mol*e))of
> the protein. Could you please give some advices how to get this value?
> >
> > Best Regards,
> > Sunisa Yoodee
> > --
> > Sunisa Yoodee, Ph.D
> >
> > Medical Proteomics Unit,
> > Faculty of Medicine Siriraj Hospital,
> > Mahidol University,
> > 6th Floor SiMR Building,
> > 2 Wanglang Road, Bangkoknoi,
> > Bangkok 10700, THAILAND
> > Tel: 66-8-06691102
> > e-mail: yd.sunisa at gmail.com
> >
> >
> > _______________________________________________
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> > ChimeraX-users at cgl.ucsf.edu
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>
>

-- 
*Sunisa Yoodee*, Ph.D

Medical Proteomics Unit,
Faculty of Medicine Siriraj Hospital,
Mahidol University,
6th Floor SiMR Building,
2 Wanglang Road, Bangkoknoi,
Bangkok 10700, THAILAND
Tel: 66-8-06691102
e-mail: yd.sunisa at gmail.com
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