It would be great if pymol was able to export
[molecules] to (the pretty recent) U3D format:
http://www.ecma-international.org/publications/standards/Ecma-363.htm
http://www.adobe.com/products/acrobat/pdfs/3d_pdf_demo.pdf
The file could then be embded into PDF using LaTeX for
example:
http://www.ctan.org/tex-archive/help/Catalogue/entries/movie15.html
I don't want to give commercial links, but this one
really has nice examples of usage of U3D:
http://www.subdo.com/default.aspx?cont=69
Mojca Miklavec
U3D is a real mess, but we're definitely working on this.
The realistic 100% open-source path to generating 3D figures appears to PyMOL -> IDTFConverter -> pdflatex
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