[Chimera-users] Surface color by electrostatic potential

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 13 09:56:39 PDT 2014


Hi Alexandra,
There should be no difference between reading of the potential files, but there are some possible differences as to why the display may look different:

(1) the molecular surface is probably slightly different in shape/size, that is, the programs probably use slightly different atomic radii for calculating the surfaces, or maybe even different algorithms (I don't know what method VMD uses to calculate surfaces).  Other variable parameters for molecular surface calculation, at least in Chimera, are probe radius (default 1.4 which is the standard value) and vertex density.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

(2) the red and blue colors set for -5 and +5 may be slightly different between the two programs

(3) Electrostatic Surface Coloring (Surface Color tool with settings intended for ESP maps) default behavior is to color by potential values 1.4 angstroms outward from the surface, not at the surface.   This is to approximate the values at the solvent-accessible surface (where the probe center goes) whereas Chimera is displaying the solvent-excluded surface (where the probe surface goes). This would tend to give smaller-magnitude values, however, since it is farther away from the atomic centers that bear the charges, so it doesn't really make sense that that could be the difference, unless you have turned that "Surface offset" option off.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>

There is no such thing as more detailed coloring given a specific potential map. You would have to calculate a new map with finer spacing to get finer detail in the potential values.  If you are really coloring by the ESP map (the dx file) the atomic charges are not used. (They would only be used to calculate the ESP map in the first place.)

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


On Aug 13, 2014, at 9:37 AM, roz orchidea <roz.orchidea at gmail.com> wrote:

> Dear all,
> 
> I am trying to get some images of the electrostatic potential surface of my complex. But I have noticed that by using the same .dx file in chimera and vmd, I am getting different coloring results. Chimera gives more negatively charged areas. I used the -5 0 5 coloring for both. Is it a difference in reading the .dx files between the 2 software? I also think that Chimera colors each side chain by the avg charge. Is it possible to have a more detailed coloring of the surface according the charges?
> 
> Thanks in advance,
> Alexandra




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