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Difference between revisions of "3d pdf"

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(rearrange some tex to avoid dropping comma)
 
Line 4: Line 4:
 
== Requirements ==
 
== Requirements ==
 
* PyMOL
 
* PyMOL
* [http://www.iaas.msu.ru/tmp/u3d/u3d-1.2.852.tar.gz u3d converter IDTF to U3D converter]
+
* [http://sourceforge.net/projects/u3d/files/Universal%203D%20Sample%20Software/ Universal 3D Sample Software - u3d converter - IDTF to U3D]
 
* LaTeX (pdflatex)
 
* LaTeX (pdflatex)
 +
 +
== Get IDFT file from PyMOL ==
 +
* Save your molecule to an IDTF file in PyMOL:
 +
<source lang="python">
 +
save pymol.idtf, *
 +
</source>
 +
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.<br>
 +
# Navigate to the '''bin''' folder: \Desktop\U3D_A_061228_5\Bin\Win32\Release <br>
 +
# 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":
 
* The following LaTeX code saved as "pymol.tex":
 
<source lang="latex">
 
<source lang="latex">
Line 30: Line 50:
 
\end{document}
 
\end{document}
 
</source>
 
</source>
 
== Directions ==
 
 
* Save your molecule to an IDTF file in PyMOL:
 
<source lang="python">
 
save pymol.idtf, *
 
</source>
 
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:
 
  ./IDTFConverter -input pymol.idtf -output pymol.u3d
 
 
 
* Create the PDF using LaTeX:
 
* Create the PDF using LaTeX:
 
   pdflatex pymol.tex
 
   pdflatex pymol.tex
 
  
 
== Caveats ==
 
== Caveats ==
Line 57: Line 62:
  
 
* 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.
 
* 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.
 
  
 
== More on 3D PDFs ==
 
== More on 3D PDFs ==
 
* [http://www.adobe.com/manufacturing/3dpdfsamples/3dsolutions/ 3D PDFs at Adobe]
 
* [http://www.adobe.com/manufacturing/3dpdfsamples/3dsolutions/ 3D PDFs at Adobe]

Revision as of 09:24, 3 March 2013

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

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

  1. Download Universal 3D Sample Software - u3d converter - IDTF to U3D, and extract to Desktop or C:\Program Files.
  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

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{center}
\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=62.45, 3Dcoo=0 0 -62.45
]{\linewidth}{\linewidth}{pymol.u3d}
\label{ex3d} A PyMOL object embedded in PDF, using U3D data format.
\end{center}
\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.

More on 3D PDFs