there are a couple TiBS articles in press on the publication of molecular
models in .pdf documents :
Kumar, et. al.
"Grasping molecular structures through publication-integrated 3D models"
http://tinyurl.com/686hvz
the 3D models are in the _supplemental_ .pdf file, so when it "doesn't
work", make sure you have that file. there are links in the article for
the right Adobe software, so check it out.
here's a direct to the supplemental pdf, but might depend on your local
subscription :
http://tinyurl.com/5awxgn
-bryan