Overview

PyMOL can convert to formats (vrml2 and idtf) that can be converted to a 3D PDF (will not work with most PDF browser plugins; must be downloaded and viewed with certain viewers liked Adobe Acrobat 9.2+).

Note. The figure is only represented in cartoon format. No sticks yet...

Requirements

PyMOL
Universal 3D Sample Software - u3d converter - IDTF to U3D
LaTeX (pdflatex)

Get IDFT file from PyMOL

Save your molecule to an IDTF file in PyMOL:

save pymol.idtf, *

PyMOL will print a line that looks like:

 3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=62.45, 3Dcoo=0 0 -62.45

copy this line into the pymol.tex file overwriting the same line in the file.

Windows - Convert the IDTF to U3D

Quick

Download Universal 3D Sample Software - u3d converter - IDTF to U3D, and extract to Desktop
Navigate to the bin folder: \Desktop\U3D_A_061228_5\Bin\Win32\Release
Copy pymol.idtf in here.
Hold shift key, right click in folder, click Open command window here.

Then copy this inot command window:

IDTFConverter -input pymol.idtf -output pymol.u3d

Copy the pymol.u3d into your LaTeX folder

General

Download Universal 3D Sample Software - u3d converter - IDTF to U3D, and extract to C:\Program Files (x86)\U3D_A_061228_5
Make a IDTF2U3D.bat and afterwards copy to C:\Windows.

@echo off
rem -- Run IDTFConverter --
set IDTF_EXE_DIR=C:\Program Files (x86)\U3D_A_061228_5\Bin\Win32\Release

if exist "%IDTF_EXE_DIR%\IDTFConverter.exe" goto haveProg
echo "%IDTF_EXE_DIR%\IDTFConverter.exe" not found
goto eof

:haveProg
if .%1==. goto noarg

"%IDTF_EXE_DIR%\IDTFConverter.exe" -input %1 -output %~n1.u3d 
goto eof

:noarg
echo no arguments given.
echo IDTF2U3D pymol.idtf

:eof
echo Done

Navigate to pymol.idtf. Right click, Open with..., Browse to: C:\Windows and select IDTF2U3D.bat

Copy the pymol.u3d into your LaTeX folder

Linux install - Convert the IDTF to U3D

Currently you have to compile the u3d converter on Linux. I did that with:
Some versions of Acrobat on Linux incorrectly parse the 3D data. Adobe knows about this and plans to fix it. Ironically, I created a 3D PDF on Linux but could only view it on Mac OS X.

See current versions here: http://www2.iaas.msu.ru/tmp/u3d

cd ~/Downloads/ ;
wget http://www2.iaas.msu.ru/tmp/u3d/u3d-1.4.3.tar.gz ;
tar -xzf u3d-1.4.3.tar.gz ;
cd u3d-1.4.3 ;
cmake . ;
make ;
chmod g+wx . ;
set IDDIR=$PWD ;

cat > IDTF2U3D << EOF
#!/bin/tcsh
set FOLD=\$PWD
set IN=\$PWD/\$1
cp -f \$IN $IDDIR
cd $IDDIR
./IDTFConverter -input \$1 -output \$1:r:t.u3d
cp -f \$1:r:t.u3d \$FOLD/
EOF

chmod +x IDTF2U3D

ln -s $PWD/IDTF2U3D ~/bin/IDTF2U3D

Then write in terminal

IDTF2U3D pymol.idtf

LaTeX code

LaTeX code pdf

Example 3D PDF
Download Example, and open in acrobat reader: 1zqa PDF

The following LaTeX code saved as "pymol.tex":

\documentclass[a4paper]{article}
\usepackage[3D]{movie15}
\usepackage[UKenglish]{babel}
\usepackage[colorlinks=true]{hyperref} 
\begin{document}
\title{PyMOL 3D Objects in PDF}
\author{Jason Vertrees}
\maketitle
\begin{figure}[!htb]
\centering
\includemovie[
poster,
toolbar, %same as `controls'
label=pymol.ud3
text=(pymol.u3d),
3Dlights=CAD,
% replace the next line with what PyMOL output
3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=243.39, 3Dcoo=0 0 -243.39
]{\linewidth}{\linewidth}{pymol.u3d}
\caption{A PyMOL object embedded in PDF, using U3D data format.}
\label{pym:ex3d}
\end{figure}
\end{document}

LaTeX beamer presentation

Download Example, and open in acrobat reader: beamer PDF
Download Example, and open in acrobat reader: beamer 1zqa PDF

\documentclass{beamer}
\usepackage[3D]{movie15}
\usepackage[UKenglish]{babel}

%% See: http://en.wikibooks.org/wiki/LaTeX/Presentations
%% See: http://www.hartwork.org/beamer-theme-matrix/
\usetheme{Copenhagen} 
\usecolortheme{beaver}

\begin{document}
\title{Simple Beamer Class}   
\author{Troels Linnet} 
\date{\today} 
\frame{\titlepage} 
\frame{\frametitle{Table of contents}\tableofcontents} 

\section{3D object} 
\frame{\frametitle{Pymol 3D object}
\begin{figure}[!htb]
\centering
\includemovie[
poster,
toolbar, %same as `controls'
label=pymol.ud3
text=(pymol.u3d),
3Dlights=CAD,
% replace the next line with what PyMOL output
3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=243.39, 3Dcoo=0 0 -243.39
]{10cm}{6cm}{pymol.u3d}
\caption{A PyMOL object embedded in PDF, using U3D data format.}
\label{pym:ex3d}
\end{figure}
}

\section{Lists}
\subsection{Lists I}
\frame{\frametitle{Unnumbered lists}
\begin{block}{My bloc}
test of bloc
\end{block}

\begin{itemize}
\item Introduction to  \LaTeX  
\item Beamer class
\end{itemize} 
}

\end{document}

Create the PDF using LaTeX:

 pdflatex pymol.tex

3d pdf

Contents