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= Overview = | = Overview = | ||
| − | PyMOL can save videos to formats (.mpg) that can be converted to a [[:File: | + | 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 | + | [[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} | ||
| + | test of bloc | ||
| + | \end{block} | ||
| + | |||
| + | \begin{itemize} | ||
| + | \item Introduction to \LaTeX | ||
| + | \item Beamer class | ||
| + | \end{itemize} | ||
| + | } | ||
\end{document} | \end{document} | ||
| Line 45: | Line 103: | ||
== See Also == | == See Also == | ||
| − | * [[3d_pdf]] | + | * [[3d_pdf | 3d protein image in pdf]] |
| − | * [[Biochemistry_student_intro#GUI_- | + | * [[Biochemistry_student_intro#GUI_-_Scene_loop | Example Scene_loop]] |
[[Category:PyMOL_in_pdf]] | [[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