Re: [Jmol-users] Molecular Electrostatic Potential - problems with charges?

[Bob H. <ha...@st...>]

cc Jmol-users as a general problem:

Problem: MEP of anions appear all one color (probably red).
or:
How to get a surface-mapped MEP isosurface to color differently.

You have to experiment. First from the popup console:

load whatever.smol #loads the model;
isosurface delete surface1 solvent mep #displays the MEP;
show isosurface #displays the JVXL data in the console

I realize this format is cryptic. Maybe I can add comments to that.
Look for the following in that file:

# isosurface delete solvent  mep
0.0 2464 3136 3136 -0.06992793 0.060803317 -0.05 0.05

The fifth and sixth  numbers, -0.0699.. and 0.0608..., are telling you 
the range of values present in the model..
The -0.05 and 0.05 are telling you the range being used for red-to-blue. 
These shown are the default values.

To change the coloring so that red-blue spans 0.0 to 0.3, for instance, 
change your command to

isosurface delete surface1 solvent color absolute 0.0 0.3 mep;

I debated setting defaults that would change with the range of values in 
the electrostatic model, but in the end I left it with defaults. The 
problem was that when you displayed an anion it had a coloration that 
didn't seem appropriate.

Bob





Nick Greeves wrote:

> Bob,
>
> I've 
> consulted http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.0#isosurface 
> but can't get it to work. I assume the command is *COLOR 
> ABSOLUTE** but none of the values I tried seemed to change the contours.*