[Chimera-users] visualizing potential with volume data

Christos Deligkaris deligkaris at gmail.com
Thu Feb 27 08:21:02 PST 2020

Thank you Elaine, now I understand better. I was under the impression
that using cube files was only consistent with the options related to
"volume data". I checked that using an offset of 0 with the
electrostatic potential option gives the same result as the volume
data value.

Related to this:  Can I use a cube file to generate an equipotential map?

Do you recommend Chimera or ChimeraX? What are the strengths of
ChimeraX currently?

Best wishes,

Christos Deligkaris, PhD
Assistant Professor of Physics

On Mon, Feb 24, 2020 at 3:22 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Dear Christos,
> If the option to color by “electrostatic potential” is chosen in the Surface Color dialog, then no matter what kind of volume data file you opened, it has the electrostatic options including offset 1.4 A.  You can click Options on the dialog to check that they are all set to the values that you want.
> The surface image you gave a link to looks the same to me as the other molecular surfaces in Chimera, in terms of shape.  The coloring is too saturated in my opinion (i.e. should have more “white” instead of all blue and red) but that is just a choice of the coloring levels, not related to the shape of the surface.  Maybe it was made a long time ago without using an offset, but I don’t know —  I didn’t make that image.
> If you want to compare what you get using the same settings, and more appropriate coloring levels in my opinion, instead take a look at the image tutorial “coloring by surface properties”:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.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 24, 2020, at 11:57 AM, Christos Deligkaris <deligkaris at gmail.com> wrote:
> >
> > dear all,
> >
> > I have obtained a cube file from NWChem with the electrostatic
> > potential around a molecule. I visualized the molecular surface using
> > Actions->Surface->Show and then colored it using the volume data
> > (followed instructions
> > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html in
> > tools->surface color (electrostatic surface coloring)) .
> >
> > Since I do not have my data stored in a potential file, can I still do
> > the surface offset? The chimera tool webpage discusses why that is
> > preferred than showing the potential on the solvent excluded surface
> > and it seems to me that option to not be available with volume data.
> >
> > Also, my surface does not look like the electrostatic potential
> > surface shown here:
> > https://www.cgl.ucsf.edu/chimera/data/tutorials/maps08/volume-basics.html
> > . The molecular surface we get with Action->Surface->Show seems to be
> > constructed with greater atomic radii than the one shown in that
> > image. I am not sure how important that is though. Is there a way to
> > ask Chimera to visualize the electrostatic potential volume data with
> > the same options Chimera would use if it was reading a Delphi, PBS
> > file?
> >
> > Best wishes,
> >
> > Christos Deligkaris, PhD
> > Assistant Professor of Physics

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