[Chimera-users] Color by electrostatic potential

[Francesco Pietra]

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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200521/e3c80790/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot_radius.png
Type: image/png
Size: 227744 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200521/e3c80790/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot_electrostatic-potential.png
Type: image/png
Size: 176684 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200521/e3c80790/attachment-0003.png>