Since there has been a good amount of discussion using Jmol to do this recently, I thought I'd mention that a paper on putting interactive 3D in PDF came out: Leaving the structural ivory tower, assisted by interactive 3D PDF Pravin Kumar, Alexander Ziegler, Alexander Grahn, Chee Seng Hee and Andreas Ziegler
Trends Biochem Sci. 2010 Jun 10. http://www.ncbi.nlm.nih.gov/pubmed/20541422 Others on the list may recall that the same first author published on this subject in TiBS in 2008. Wayne
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