[Chimera-users] Color by electrostatic potential

[Francesco Pietra]

Hi Elaine
Were not that yesterday morning, by opening the cube file (and then acting
in a way that I have not annotated) the surface became colored for
electrostatic potential, i would now say that the cube file, as obtained
with the python script mep.py from ORCA data, is not fully understood by
CHIMERA.

I followed now your last indications, going through the steps illustrated
in the attached screenshot. I was now through the same steps as yesterday
afternoon: by clicking "Color", all the surface becomes milk white. With
"Uncolor" back to the actual screenshot view.

I am really sorry for still being unable to raise colors for the
electrostatic potential. It is like if I were in a mental loop.

Best
francesco

On Thu, May 21, 2020 at 8:41 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Francesco,
> I wasn't sure if you were trying to color the molecular surface, or to
> show isopotential surfaces. My previous instructions were for isopotential
> contour surfaces.
>
> Here are the instructions for coloring the molecular surface instead:
>
> 1. Hide all contour surfaces in Volume Viewer (e.g. command "volume all
> hide")
>
> 2. Show the molecular surface (e.g. command "surface")
>
> 3. Use Tools... Structure Analysis... Electrostatic Potential Coloring and
> make sure you choose the molecular surface as the one to color.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html
> >
>
> This tutorial includes coloring the molecular surface using an
> electrostatic potential file (see the last section):
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#esp2
> >
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On May 21, 2020, at 10:48 AM, Francesco Pietra <chiendarret at gmail.com>
> wrote:
> >
> > Hi Elaine
> > From Volume Viewer .. open map I opened the cube file. Ctrl-click on the
> histogram simply added another black bar. Coloring surface gave two colors
> with option "radius", single color with option "electrostatic-potential'
> (the cube file was built for the latter).
> >
> > I can't realize where I am wrong. This morning I had a beautiful
> red-white-blue coloring fitting for what I expected as to electrostatic
> interactions, and the files are the same, downloaded from the remote
> cluster for chimera examination.
> >
> > thanks for advice
> > francesco
> >
> > On Thu, May 21, 2020 at 6:41 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Francesco,
> > I guess you mean isopotential contour surfaces.
> >
> > I believe if you open signed data, then Volume Viewer would
> automatically show two contour surfaces, one for positive and one for
> negative.  However, if it is only showing one contour surface, just
> Ctrl-click on the histogram in Volume Viewer to add another one (or as many
> more that you would like), as indicated by another vertical bar.  You can
> drag the vertical bars on the histogram to change the levels, and change
> the color of the one most recently dragged or clicked.
> >
> > These vertical bars are called "thresholds" in the documentation.
> >
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html
> >
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#display
> >
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> > > On May 21, 2020, at 8:52 AM, Francesco Pietra <chiendarret at gmail.com>
> wrote:
> > >
> > > I was able to open with chimera 1.1.3.1 (linux)
> electrostatic-potential cube files generated from ORCA package and view
> them in colors (red lowest, blue highest potential). I can't remember how I
> succeeded and now, from chimera help, I am no more able. Only a single
> color.
> > > Thanks for putting me on the right way.
> > > chiendarret
> >
> >
> <Screenshot_radius.png><Screenshot_electrostatic-potential.png>_______________________________________________
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>
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