[PyMOL] electrostatic potential

[Leroy L. <lav...@ch...>]

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 
<http://www.chem.ucsb.edu/%7Elaverman/Freeman/ESP2.html> and some short 
animations here: http://www.chem.ucsb.edu/~laverman/Freeman/ESP.html 
<http://www.chem.ucsb.edu/%7Elaverman/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)/
level/ = 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/

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:


/isosurfacedens 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