[Chimera-users] Contour mapping
meng at cgl.ucsf.edu
Sun Apr 29 10:17:12 PDT 2012
It might make more sense to color by electrostatic potential (ESP) than by partial charges. You could either use Chimera's "Coulombic Surface Coloring" to calculate Coulombic ESP, or use a separate continuum electrostatics program such as APBS or DelPhi to calculate an ESP map (values on a grid). In Chimera, molecular surfaces can be color-coded by the ESP map values, or the ESP can instead be shown as isopotential contour surfaces. My thinking is that the ESP is less noisy (smoother spatially) and better represents the electrostatic environment than all the atomic partial charges, and using consistent color-coding, or consistent isopotential values in the case of contour surfaces, allows comparison among different structures.
Relevant tools are Coulombic Surface Coloring (command "coulombic") and Electrostatic Surface Coloring (command "scolor").<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html>
This tutorial includes coloring the molecular surface by Coulombic ESP:
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Apr 29, 2012, at 7:49 AM, Nikolay Igorovich Rodionov wrote:
> Hi all,
> I was wondering if anyone could help me create an accurate contour map based on surface charge. I’ve tried rendering my molecule by charge, then using the surface clipping, capping, and the color zone tools. However, the coloring varies based on how I orient the plane. Does anyone know a better and more accurate way to creating a contour map?
> Nikolay Rodionov
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