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
• 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.

Convert the IDTF to U3D

1. Download Universal 3D Sample Software - u3d converter - IDTF to U3D, and extract to Desktop or C:\Program Files.
   
2. Navigate to the bin folder: \Desktop\U3D_A_061228_5\Bin\Win32\Release
   
3. Copy pymol.idtf in here.
4. 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

LaTeX code

• 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}

• 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.

Linux install

(This section is not working. How to build this ???)

unzip U3D_A_061228_5.zip
cd ~/Downloads/U3D_A_061228_5/Source
setenv U3D_SOURCE $PWD/
#Comment win, uncomment Linus lines
nano $U3D_SOURCE/Config/u3d.conf
setenv U3D_LIBDIR {$U3D_SOURCE}Build/U3D
setenv PATH ${PATH}:{$U3D_LIBDIR}
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:{$U3D_LIBDIR}

alias IDTFConverter $PWD/IDTFConverter.exe

More on 3D PDFs

• 3D PDFs at Adobe

See Also

• Movie in pdf