[Chimera-users] Electrostatic Potential
Tom Goddard
goddard at sonic.net
Fri Jan 3 10:17:09 PST 2020
Hi Fernando,
The print statement I suggested you add to the Chimera surface color code gives the electrostatic potential values 1.4 Angstroms out from the surface while the surfval.py script from the Chimera Python scripts page gives the values on the surface. The 1.4 Angstrom offset is described in the Surface Color tool documentation
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html <https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
and that offset parameter is shown in the Options panel of the Surface Color dialog.
Tom
> On Jan 2, 2020, at 9:22 PM, Fernando Villa <fer.vdl1928 at gmail.com> wrote:
>
> Dear Elaine.
>
> Thank you very much, I really appreciate it.
> I am confused with some data.
> A few months ago Tom Goddard sent me a phyton code to get the vertex coordinates and the values in Reply log:
>
> In Windows:
> 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
>
> To obtain the output vertex coordinates and potential values:
> 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>Click color
> = All values Appear in reply log (attached file: 001_xyz-val_ESP.txt)
> <imagen.png>
> I suppose that the first three numbers are the vertex coordinates and the last value is the ESP Coulombic (Kcal / mol.e).
>
> Value at mouse position:
> > Surface color> Options
> > Check the box Report value at mouse position
> > Click color:
> <imagen.png>
> All the electrostatic potential values appear by Coulombic [Kcal / (mol.e)] at the mouse position, I suppose they are the same values shown in replylog = file 001_xyz-val_ENG.txt.
>
> However, when I open the surfval.py script
> Command:
> surfvalues # 0.1 # 1 ~/Desktop /002_xyz-val_script-val_ENG.txt
>
> A file is saved (attached file: 002_xyz-val_script-val_ESP.txt) with the same vertex coordinates. The ESP values in Kcal/(mol.e) are different from 001_xyz-val_ESP.txt.
> <imagen.png>
>
> Besides, if I save the values from Volume viewer:
> Volume viewer> Tools> Values at atom position
> > Click Histogram> Render / Select by attribute
> > File> Save attribute> Click box “Restrict save to current selection, if any”> File name: 003_ at val_ENG.txt <mailto:003_ at val_eng.txt>> Save (attached file:003_ at val_ENG.txt <mailto:003_ at val_eng.txt>)
> The ESP values --> Kcal/(mol.e)
>
> My question is:
> The files 001_xyz-val_ESP.txt, 002_xyz-val_script-val_ENP.txt, 003_ at val_ESP.txt <mailto:003_ at val_esp.txt>, and the values at mouse position have units in Kcal/(mol.e)?
>
> If I'm wrong, let me know please.
>
> Regards.
>
> Fer.
>
>
> El lun., 30 de dic. de 2019 a la(s) 11:56, Elaine Meng (meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>) escribió:
> 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 <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>>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html#volume <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html#volume>>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html <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/016139.html>>
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016159.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 <mailto: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 <mailto: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 <mailto: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
> >>>
>
> <003_ at val_ESP.txt><001_xyz-val_ESP.txt><002_xyz-val_script-val_ESP.txt>_______________________________________________
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