[Chimera-users] visualizing potential with volume data

Fri Mar 6 10:22:40 PST 2020

Thank you Elaine, with your explanations and Chimera documentation I
was able to visualize my results.

Is it possible to visualize the electric vector field from a cube file
with the electrostatic potential?

Best wishes,

Christos Deligkaris, PhD
Assistant Professor of Physics

On Thu, Feb 27, 2020 at 12:31 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> Hi Christos,
> For electrostatic potential (regardless of input file format) it is recommended to use an offset of 1.4 Angstroms for coloring a molecular surface, as discussed in this recent post:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-February/016514.html>
>
> Yes, any volume data (values on a 3D grid) including electrostatic potential, density, etc. read from any volume data format can be shown as isosurfaces.  Just don’t use the Surface Coloring tool.  Use the Volume Viewer tool, style “surface” or “mesh” … if you open one of the formats automatically recognized as electrostatic potential, the contour surfaces are hidden  and the Surface Color dialog is shown.  Just dismiss the Surface Color dialog and start Volume Viewer (Tools… Volume Data… Volume Viewer) and show the contour surfaces by clicking the small “eye” icon (oval) to the right of the step value. It may take several seconds to read the electrostatic potential and display it after you click the icon, depending on the size of the file.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
>
> (I believe the isopotential (contour) surfaces are what is shown automatically when you open a cube file anyway.)  Then in Volume Viewer you can move the thresholds (vertical bars) horizontally along the data histogram to change the contour levels, click the square color well to change colors, etc. as explained here:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsurf>
>
> Whether I recommend Chimera or ChimeraX depends on what you are trying to do.  Generally I would recommend having both.  There is nothing to stop you from having both and using whichever one suits you for a given task: each does some things the other does not, at least yet.  I mostly use ChimeraX and find its commands are easier to remember, but also I need to use it more because I write documentation for new features.
>
> Some of the main advantages of ChimeraX vs. Chimera are listed here:
> <http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html>
>
> For features still missing from ChimeraX, see “missing features” in the download page:
> <http://www.rbvi.ucsf.edu/chimerax/download.html>
>
> We are actively developing ChimeraX, so it will have more capabilities nearly every day.  You can scan through the “feature highlights” and more comprehensively, take a look at the tools and commands listed in the User Guide index:
> <http://www.rbvi.ucsf.edu/chimerax/features.html>
> <http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html>
>
> There is also a Toolshed web repository for ChimeraX plugins:
> <https://cxtoolshed.rbvi.ucsf.edu/>
>
> 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 27, 2020, at 8:21 AM, Christos Deligkaris <deligkaris at gmail.com> wrote:
> >
> > 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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>