[Chimera-users] Coloring electrostatic potential

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 3 12:01:21 PST 2012

Hi George,
I'm still not clear on what you mean by "show," but here are a couple possibilities...

If you want isopotential contour surfaces, you would use the Volume Viewer interface (in menu under Tools... Volume Data).  You may need to click on the histogram of the potential values in that tool to get an initial (isopotential) surface display.  In that tool, you can move a slider on the histogram to control the contour level, change its color, and have multiple sliders of different colors for multiple levels.  Anyway, much too much to describe here, but it's all documented in the Volume Viewer page:

If you want to color the spheres by potential values, you would use Values at Atom Positions (also under Tools... Volume Data).  In that tool, you would choose the Molecule (your spheres model) and the Volume data (that would be the electrostatic potential map), then click Histogram to bring up Render by Attribute.  In Render by Attribute you can then control coloring the atoms by the associated potential values.

Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 3, 2012, at 11:25 AM, George Tzotzos wrote:

> Apologies for the earlier message, I wasn't clear enough. I'm able to color the "spheres" by selecting them as atoms and colouring them red and blue. My question was how to render the electrostatic potential around the spheres.
> Thanks and sorry about the confusion
> George
> On Feb 3, 2012, at 8:10 PM, George Tzotzos wrote:
>> Hi everybody,
>> I'm using SiteHound for ligand binding identification sites. I'm comparing the highest affinity sites for two superimposable receptors. I'm attaching an example where the sites favourable to protein 1 are shown red, whereas those for protein two blue.
>> I've opened in Chimera the file that contains the red and blue clusters (difference.pdb) as well as the corresponding potential file (potential.dx). I used the Volume Viewer to different affinity areas but had .... no luck.
>> Any help would be greatly appreciated
>> Best regards
>> George

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