[Chimera-users] Electrostatic Potential
Fernando Villa
fer.vdl1928 at gmail.com
Mon Jan 6 21:39:27 PST 2020
Thank you very much Dr. Elaine, it has helped me a lot, I really
appreciate it ..
best regards.
Fer.
ATTE
Fernando Villa Díaz
El vie., 3 de ene. de 2020 a la(s) 11:02, Elaine Meng (meng at cgl.ucsf.edu)
escribió:
> Dear Fernando,
> The values are in whatever units are in the map file. So you would look
> in the documentation for the program that made the map (APBS, DelPhi, …) to
> find out what the units are.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > 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> Save (attached file:
> 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, 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) 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>
> >
> > 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
> > >>>
> >
> > <003_ at val_ESP.txt
> ><001_xyz-val_ESP.txt><002_xyz-val_script-val_ESP.txt>_______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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