Hi Dirk -
I would do this the basic way (because that's the only way I know). Write a PyMOL script - not a python script, just a series of PyMOL commands. Like this:
(whatever commands you need to load and position your molecules and draw the surfaces)
set transparency=0.05, your_ligand
set transparency=0.1, your_ligand
Setting transparency to 1 is fully transparent, i.e. invisible. Transparency=0 is opaque. Once you've run this script, which you can invoke from the PyMOL command line by typing "run my_script", you'll have a series of image files showing the fade. I recommend using Quicktime Pro to fuse them into a movie - it only costs $30, and it's easy to use for this purpose.
Hope that helps,
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems,
a wholly owned subsidiary of Eli Lilly & Company
180 Varick Street, 6th floor
New York, NY 10014