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(Created page with "= Overview = PyMOL can save videos to formats (.mpg) that can be converted to a movie PDF (will not work with most PDF browser plugins; must be download...")
 
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= Overview =
 
= Overview =
PyMOL can save videos to formats (.mpg) that can be converted to a [[:File:Pymol_movie.pdf|movie PDF]] (will not work with most PDF browser plugins; must be downloaded and viewed with certain viewers liked Adobe Acrobat 9.2+).
+
PyMOL can save videos to formats (.mpg) that can be converted to a  
 +
[[:File:pymol_movie|movie PDF]]
 +
(will not work with most PDF browser plugins; must be downloaded and viewed with certain viewers liked Adobe Acrobat 9.2+).
  
 
== Requirements ==
 
== Requirements ==
Line 9: Line 11:
 
* Save a '''.mpg''' file from your video. <br>
 
* Save a '''.mpg''' file from your video. <br>
 
You can try this tutorial: <br>
 
You can try this tutorial: <br>
[Biochemistry_student_intro#GUI_-_Scene_loop Scene_loop]
+
[[Biochemistry_student_intro#GUI_-_Scene_loop | Example movie]]
  
 
== LaTeX code ==
 
== LaTeX code ==
 +
Download Example, and open in acrobat reader: [http://www.fys.ku.dk/~tlinnet/movie.pdf movie PDF] <br>
 +
Note, the resolution of the movie, has been cut intentionally to save filesize.<br>
 +
Download Example, and open in acrobat reader: [http://www.fys.ku.dk/~tlinnet/movie_highres.pdf movie PDF High Resolution] <br>
 
* The following LaTeX code saved as "pymol.tex":
 
* The following LaTeX code saved as "pymol.tex":
 
<source lang="latex">
 
<source lang="latex">
Line 35: Line 40:
  
 
See movie \ref{mov:ex3d}
 
See movie \ref{mov:ex3d}
 +
 +
\end{document}
 +
</source>
 +
 +
== LaTeX beamer presentation ==
 +
Download Example, and open in acrobat reader: [http://www.fys.ku.dk/~tlinnet/beamer_movie.pdf beamer movie PDF] <br>
 +
Note, the resolution of the movie, has been cut intentionally to save filesize. <br>
 +
Download Example, and open in acrobat reader: [http://www.fys.ku.dk/~tlinnet/beamer_movie_highres.pdf beamer movie PDF High Resolution] <br>
 +
<source lang="latex">
 +
\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{Movie}
 +
\frame{\frametitle{Pymol Movie object}
 +
 +
\begin{figure}[!htb]
 +
\centering
 +
\includemovie[
 +
poster,
 +
toolbar, %same as `controls'
 +
text={\small(Click to play movie)}
 +
]{10cm}{6cm}{movie.mpg}
 +
\caption{A PyMOL movie object embedded in PDF, using mpg format.}
 +
\label{mov:ex3d}
 +
\end{figure}
 +
 +
}
 +
 +
\section{Lists}
 +
\subsection{Lists I}
 +
\frame{\frametitle{Unnumbered lists}
 +
\begin{block}{My bloc}
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test of bloc
 +
\end{block}
 +
 +
\begin{itemize}
 +
\item Introduction to  \LaTeX 
 +
\item Beamer class
 +
\end{itemize}
 +
}
  
 
\end{document}
 
\end{document}
Line 43: Line 101:
 
== More on movies in PDFs ==
 
== More on movies in PDFs ==
 
* [http://pages.uoregon.edu/noeckel/PDFmovie.html PDFmovie]
 
* [http://pages.uoregon.edu/noeckel/PDFmovie.html PDFmovie]
 +
 +
== See Also ==
 +
* [[3d_pdf | 3d protein image in pdf]]
 +
* [[Biochemistry_student_intro#GUI_-_Scene_loop | Example Scene_loop]]
 +
 +
[[Category:PyMOL_in_pdf]]

Latest revision as of 02:00, 28 March 2014

Overview

PyMOL can save videos to formats (.mpg) that can be converted to a movie PDF (will not work with most PDF browser plugins; must be downloaded and viewed with certain viewers liked Adobe Acrobat 9.2+).

Requirements

  • PyMOL
  • LaTeX (pdflatex)

Get .mpg file from PyMOL

  • Save a .mpg file from your video.

You can try this tutorial:
Example movie

LaTeX code

Download Example, and open in acrobat reader: movie PDF
Note, the resolution of the movie, has been cut intentionally to save filesize.
Download Example, and open in acrobat reader: movie PDF High Resolution

  • 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{Troels Linnet}
\maketitle

\begin{figure}[!htb]
\centering
\includemovie[
poster,
toolbar, %same as `controls'
text={\small(Click to play movie)}
]{320px}{216px}{movie.mpg}
\caption{A PyMOL movie object embedded in PDF, using mpg format.}
\label{mov:ex3d}
\end{figure}

See movie \ref{mov:ex3d}

\end{document}

LaTeX beamer presentation

Download Example, and open in acrobat reader: beamer movie PDF
Note, the resolution of the movie, has been cut intentionally to save filesize.
Download Example, and open in acrobat reader: beamer movie PDF High Resolution

\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{Movie} 
\frame{\frametitle{Pymol Movie object}

\begin{figure}[!htb]
\centering
\includemovie[
poster,
toolbar, %same as `controls'
text={\small(Click to play movie)}
]{10cm}{6cm}{movie.mpg}
\caption{A PyMOL movie object embedded in PDF, using mpg format.}
\label{mov: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

More on movies in PDFs

See Also