It is indeed possible to get Jmol to work with a passive 3d setup,
i.e. 
using two projectors polarized perpendicular to each other and
a non-depolarizing screen. 

Set up graphics display on the laptop to extended mode for the
external VGA 
signal and open a Jmol page in the extended display
area, invoke the 
side-by-side stereo display mode (cross-eyed or
wall-eyed.. one of these 
will be correct depending on your
connections) and one side will go to
one projector, the other side to
the other projector. The built-in 
laptop screen can be used for the
script window while the Jmol page 
displays on the external
screen...very convenient. This gadget is not 
expensive...CDW sells
analog version for $149
Thanks for the responses!  The setup I'm working with 
already works with DS Viewer Pro (we have the proper video card, silver 
screen, and 3d glasses).  I will definitely try this new way to get
the  cross-eyed/wall eyed views to work.  Just to confirm, I should
'extend  the desktop' and open a Jmol on the extended screen.  I'm
concerned that  this will simply show 2 side-by-side images, just like
when you select  this stereographic mode on the monitor (as opposed to two
overlapping  images, one of a slightly different angle).
 
Here
is the setup I'm working with: 
http://chemed.chem.pitt.edu/3DProjection/technical.htm
It would be great to show a 3D animation of an enolation or similar rxn
before the semester ends!
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