3d pdf
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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
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
LaTeX code
Example 3D 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
\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
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 ???)
sudo yum install perl-XML-Parser perl-XML-Simple
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}
cd $U3D_SOURCE/Tools/BuildSystem
chmod +x build.sh
./build.sh release
alias IDTFConverter $PWD/??