From: Bob Hanson <hansonr@st...> - 2006-12-15 16:49:25
cc Jmol-users as a general problem:
Problem: MEP of anions appear all one color (probably red).
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.
Nick Greeves wrote:
> 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.*