In case you are interested, Jim, Jmol will read (most/some) PyMOL session
files, and Jmol can then create both an idtf for generating a u3d file, and
a small sample TeX file also that can be used to create a PDF containing
it.
I had some interest in u3d back in 2009, when I wrote this exporter. You
might be interested in my notes at the top of
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/export/_IdtfExporter.java
Here are a few examples created using Jmol:
http://chemapps.stolaf.edu/jmol/u3d/
As I recall, the TeX file is necessary in order to properly reproduce the
viewport state.
My conclusion was that u3d is an absolutely unmanageable file format. Its
construction is totally obtuse, and the idtf->u3d converter has bugs that
will probably never be fixed. I could be wrong, and in the intervening
years it has improved, but my impression at the time was that it was an
experimental format out of Adobe's research labs that never really made it
and hasn't been developed much since then.
Its inclusion in PDF file quite frankly takes the "P" out of "PDF."
Bob Hanson
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