Hello Arne -
I've been generating quite a lot of these types of figures lately for a textbook and wrote myself a list of steps as I can never seem to remember all the commands.  I've copied and pasted my notes below - hopefully this will be helpful.  For your specific issue, I suspect you are creating the isosurface from the electrostatic potential cube file.  If so then you will always get a single color because the isosurface you've created has a single electrostatic potential value.  You need two cube files to make the image.  Create the isosurface from the electron density cube file, then color it with the electrostatic potential cube file. 

You might also look at the volume rendering of the electrostatic potentials.  There are some static images here:
http://www.chem.ucsb.edu/~laverman/Freeman/ESP2.html and some short animations here: http://www.chem.ucsb.edu/~laverman/Freeman/ESP.html

For surface electrostatic plots in PyMOl


   Load the dens and esp cube files, then run this command:

isosurface name, map, level


name = name to call the new surface  (I typically call this dens)     
map = name of the map source (i.e. the cube file name)
= contour level (use 0.02 as a good starting value, adjust up or down to get the isosurface you want)


Create a new color map


ramp_new name, source, [-.05,-0.025, 0,0.025, .05], [red,orange, yellow,green, blue]


name = name of the color ramp  (I use “spectrum” as a name)

source = the esp cube file source

alter the values in the first vector to match the molecule (see jmol bits below)


color the density surface


set surface_color, color, selection


color = name of the color ramp (“spectrum”)

selection = name of the density isosurface  (“dens”)



Rebuild to see the colors if they do not show up.

Setting the color range


To extract the range of values on a given isosurface when generating the color ramp I use jmol to get the numbers:

If anyone knows how to do this in pymol that would be great.


In jmol run the following from the console:

isosurface  dens 0.02  "C:/…/dens.cube"  color absolute -0.1 0.1  "C:/…/ esp.cube" 


where dens.cube and esp.cube are the paths to the electron density and electrostatic potential files.


The max and min values will be displayed on the console.  Go back to pymol and divide this range by 4 to set the color scale for the esp color ramp.

Leroy Laverman
University of California, Santa Barbara