[Chimera-users] Color surface by electrostatic potential vs color by value at atom position

Yu Zhou mr_yuzhou at yahoo.com
Fri Feb 21 17:50:45 PST 2020

 Many thanks for you prompt reply, which is very helpful to me.


    On Friday, February 21, 2020, 07:28:18 PM CST, Elaine Meng <meng at cgl.ucsf.edu> wrote:  
 Hi Yu Zhou,
The electrostatic potential coloring default is to use values calculated 1.4 Angstroms outward from the molecular surface (at approximately the solvent-accessible surface).  You can see or change this “offset” value if you click the Options button on the Surface Color tool.  However, even if you set offset to 0, it will be evaluating the value at the molecular surface.

The default offset of 1.4 is recommended for coloring by electrostatic potential, however, which is why we made it the default.  The solvent-accessible surface is approximately how close the center of a ligand atom could get to the protein and represents what an interacting molecule would “see."

Values at atom positions gets the values at the atomic centers of the protein, which are inside the surface.  You definitely should not use those values because the potential exactly at the same position as a charge (which is placed at the atomic center) is a spike, essentially a singularity, that does not represent what a molecule interacting with the protein would “see.”  In other words, a ligand atom would never be placed at exactly the same position as an atom in the protein. It does not make any sense to use this approach for coloring by electrostatic potential.

There is a diagram here showing the relationship between the atoms of the protein, molecular surface, and solvent-accessible surface.  The molecular surface is the one displayed by Chimera.

I hope this clarifies the situation,
Elaine C. Meng, Ph.D.                      
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 21, 2020, at 5:13 PM, Yu Zhou <mr_yuzhou at yahoo.com> wrote:
> Hi there,
> I want to color protein surface by electrostatic potential data calculated using APBS 1.5. I tried two methods in Chimera and got quite different results. The resulted images can be found in attachment. 
> In the first attached figure (fig1_ep surface) the surface was colored by the “Electrostatic Surface Coloring” tool, in the second attached figure (fig2_value atom) the surface was colored by the “Values at Atom Positions” tool. Same color palette (red: -35, white: 0, blue: +35) and potential file was used in both cases.
> Thanks for your help.
> Yu Zhou
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