[Chimera-users] Color by electrostatic potential
meng at cgl.ucsf.edu
Fri May 22 08:29:51 PDT 2020
You are still showing the volume surface and trying to color the volume surface. That is the wrong surface. You need to hide volume surface (step #1 in previous message), show molecular surface (step #2), and in then in the Surface Color dialog, choose the *molecular* surface as the surface to color (step #3).
Your picture of the Surface Color dialog shows "Color surface [the cube file model]" which is the volume surface, not the molecular surface. You have to change that to your molecular surface model.
Below that shows "Electrostatic potential [the cube file model]" which is correct.
Chimera does understand cube files. However, this format is also used for orbitals, spin density, etc. so the default display is as volume isosurfaces. As I said, you would just hide that display and then carry on as usual for electrostatic potential. This is all explained in the tutorial:
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On May 22, 2020, at 2:19 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> 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.
> 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.
> This tutorial includes coloring the molecular surface using an electrostatic potential file (see the last section):
> I hope this helps,
> 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 188.8.131.52 (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
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