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
- Download Universal 3D Sample Software - u3d converter - IDTF to U3D, and extract to Desktop or C:\Program Files.
- 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
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.
Linux install
unzip U3D_A_061228_5.zip cd ~/Downloads/U3D_A_061228_5/Bin/Win32/Release/ chmod +x IDTFConverter.exe alias IDTFConverter $PWD/IDTFConverter.exe
- 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.