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+).

Note. The figure is only represented in cartoon format. No sticks yet...

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.

Windows - Convert the IDTF to U3D

Quick

1. Download Universal 3D Sample Software - u3d converter - IDTF to U3D, and extract to Desktop
   
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

General

1. Download Universal 3D Sample Software - u3d converter - IDTF to U3D, and extract to C:\Program Files (x86)\U3D_A_061228_5
   
2. 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

1. Navigate to pymol.idtf. Right click, Open with..., Browse to: C:\Windows and select IDTF2U3D.bat

Copy the pymol.u3d into your LaTeX folder

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

Download zip

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

### ERROR???? ###
Building Core 
---- Build started: Project: Base, Configuration: release Lin32 -----
In file included from IFXVectorHasher.cpp:32:
IFXVectorHasher.h: In member function ‘BOOL IFXVectorHasherNodeIterator::Next()’:
IFXVectorHasher.h:215: error: cast from ‘IFXVectorHasherVectorNode*’ to ‘BOOL’ loses precision
IFXVectorHasher.h: In member function ‘BOOL IFXVectorHasherBinIterator::Next()’:
IFXVectorHasher.h:279: error: cast from ‘IFXVectorHasherBinNode*’ to ‘BOOL’ loses precision
make: *** [all] Error 1
Base - 2 error(s), 0 warning(s) 
*********** BUILD Core ERROR  ************* 
------------------- Build done -------------------
Base - 2 error(s), 0 warning(s) : failed
--------------------------------------------------
Entire build: 0 succeeded, 1 failed
=====================================
ERROR, build process is not complete
=====================================
#####################

alias IDTFConverter $PWD/??

LaTeX code

LaTeX code pdf

Example 3D PDF
Download Example, and open in acrobat reader: 1zqa 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
Download Example, and open in acrobat reader: beamer 1zqa 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

More on 3D PDFs

• 3D PDFs at Adobe
• Future of scientific publishing

See Also

• Movie in pdf