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)


png movie_001.png

set transparency=0.05, your_ligand


png movie_002.png

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

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