Hi David,
 
This has already been done with PyMOL.  There's a video at:
 
http://molviz.cs.toronto.edu/molviz/
 
and the code is downloadable.
 
The stereo effect isn't so great with both eyes open, but I do think there is potential for use of head or object tracking as a means of controlling rotation.
 
Cheers,
Warren

From: CCP4 bulletin board on behalf of David Roberts
Sent: Wed 5/14/2008 12:59 PM
To: [log in to unmask]
Subject: [ccp4bb] While on the subject of stereo

OK, so we weren't on this subject, and all of you are tired of me
asking.  However, the following link came to me and I wanted to see some
programmers opinions on this one.  The thing I'm wondering is, what
needs to be done on the programming end to make this something that we
could use in a classroom to show molecules in stereo.  It seems like it
would be fun, and I actually think it would work well, though I don't
know if it would work with more than one person looking at the screen at
a time (now that I really think about it, probably not - nevermind).  If
it only works with one person, can we use this for modeling?

Just curious

www.ted.com/index.php/talks/view/id/245

Dave