I recently came across this
paper on embedding interactive 3D graphics in pdf files. Unfortunately, I couldn't animate the 3D figures, and I wrote the author (Vlad Vasilyev) who kindly wrote back that:
(1) the publisher (Springer) is a bit behind the times so the interactive figures are found in the supplemental material, but
(2) the ACS is more on the ball, as can be seen in
this paper (this is the one I use in the screencast), and
(3) he has made a bunch of tutorials on how to create such diagrams on
this page.
This page also contains some pdf files with 3D graphics you can play around with if you don't have access to the papers. Be sure to use Adobe Acrobat Reader 9.
Note that it is also possible to include animations such as
vibrational motion (NB: 16 MB file)
Very cool! I haven't tried this myself, but you can be sure I will. Unfortunately, it seems that you need a piece of commercial software (Adobe Acrobat 9 Pro Extended) to do this.
On a related note, check you
the interactive figure of interactive figures created by fellow blogger
Henry Rzepa (please give the page some time to load).