3d pdf

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+).

Requirements

• PyMOL
• u3d converter IDTF to U3D converter
• LaTeX (pdflatex)
• 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{center}
\includemovie[
        poster,
        toolbar, %same as `controls'
        label=pymol.ud3
        text=(pymol.u3d),
        % replace the next line with what PyMOL output
        3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=62.45, 3Dcoo=0 0 -62.45,
        3Dlights=CAD,
]{\linewidth}{\linewidth}{pymol.u3d}
\label{ex3d} A PyMOL object embedded in PDF, using U3D data format.
\end{center}
\end{document}

Directions

• 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

save this line for later.

• Convert the IDTF to U3D:

 ./IDTFConverter -input pymol.idtf -output pymol.u3d

• Copy the line that looks like

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

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

• Create the PDF using LaTeX:

 pdflatex pymol.tex

Caveats

• Currently you have to compile the u3d converter on Linux. I did that with:

cmake .
make

which created "IDTFConverter" that I used above.

• 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.

More on 3D PDFs

• 3D PDFs at Adobe