That is a cool feature, and is kind of the "future" of publishing. :-)
Or at least, a very powerful tool for teaching.

But it is sad that it only have cartoon export.
I wish that it could include other representations.

For now I use Jmol, which can export the whole representation in the window.
I can import small molecules through. Files->Get MOL-> And then CAS number or smiles.
For proteins I scoop into, and find the protein in the Jmol online viewer. (Just changing to white back ground).

Right click in Jmol window->Export file->Export IDTF 3D model.

That saves a .idtf file, and a .tex file ready for LaTeX.
Rename the .idtf file, so it only ends on .idtf and not:

Simpy converting the .idtf to .u3d as instructed in,
and you are ready to go from the given .tex file. (Removing the last looong comment section.)

With a little practice, it only takes 3 min, to have 3d implementation of your molecule
in teaching material / beamer presentation.

I wish that could be implemented in PyMOL, and I have been looking for a wish list,
but I don't know where that exists?


Troels Emtekær Linnet
Ved kløvermarken 9,
2300 København S
+45 60210234

2013/3/12 Mooers, Blaine H.M. (HSC) <>
I saw Jason Vertrees update of
It has the address to the source code for u3d-1.4.3. I could not compile earlier
versions of this program on a Mac running Snow Leopard, but I had
success with this version. I followed Jason's directions for compiling on
Linux through  chmod g+wx. I had installed cmake earlier.

The program compiles fine on Ubuntu 12.04 too.

I used pdflatex from fink with beamer and the movies15 package.

Blaine Mooers
Assistant Professor
Director Macromolecular Crystallography Lab
Member Stephenson Cancer Center
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466

Letter address:
P.O. Box 26901, BRC 466
Oklahoma City, OK 73190

 Shipping address:
 975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910


Faculty webpage:
lab webpage:
SAXS Links webpage:

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