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)
ray
png movie_001.png
set transparency=0.05, your_ligand
ray
png movie_002.png
set transparency=0.1, your_ligand
etc.
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,
Matt
--
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
phone:(917)606-4116 fax:(212)645-2054
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