[Chimera-users] Electrostatic Potential

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 16 14:28:52 PDT 2019

Hi Fernando,
This is not answering your specific request, but some points that may be important to consider:

(1) Electrostatic potential (the values in dx files) is not the same as charge.  Maybe you already know that, but I’m just making sure it is clear.  The charge on each atom is already in the pqr file, so if you just wanted the total charge of the molecule, you would add those up.  You could even select the surface atoms only, and then add their charges.

(2) maybe it is not meaningful to count points that have electrostatic potential values very close to zero.

(3) similarly, maybe it is not meaningful to consider points with very small values as having equal importance as points with very large values (that is what you are doing if you only care about the sign)

(4) the spatial distribution of the values is important for molecular recognition, not just the number of points with some value. It is very different to have positive and negative intermixed all over the molecule, as compared to positive concentrated on one end of the molecule and negative concentrated on the other end, but those two situations might give identical % areas in your calculation.

I understand what you want, but I’m concerned it may not be biologically/physically meaningful.
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

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