3D PDF Tutorial

This tutorial describes how to embed 3D, interactive molecules into Adobe PDFs. These files can be uploaded as supplemental material along with your JLR paper.

For this tutorial we're going to use Adobe Acrobat Pro 9 Extended and Pymol v. 0.99, a 3D visualization tool. Both of these programs are available for trial periods.

Adobe's 3D-capture utility should allow you to capture and embed a 3D model from any program that uses OpenGL, the current standard for 3D programs.

This method can be used to embed a wide variety of 3D objects or data sets, including Z-stacks from confocal laser scanning microscopy, or single particle cryo-EM reconstructions modeled with programs like Chimera.


  • First obtain a PDB file from the PDB database.
  • Save it to the desktop.
  • Open the PDB file in Pymol.
  • Adjust the display setting to maximum quality.
  • You can adjust the molecule however you see fit. For this demonstration we're going to use a preset called "pretty."
  • Alternatively, you could run your favorite Pymol script to display your model the way that you like.
  • Now we move over to Adobe Acrobat Pro 9 Extended.
  • First go to file, then choose create a PDF from 3D capture.
  • The 3D capture feature allows it to import the 3-D data from other programs using the "print-screen" button.
  • The pop-up tells you to click back to Pymol and press "print screen"
  • After a few seconds, click back to Adobe and adjust your import settings. Make sure the detail level is high. Click Ok when it tells you "this might take a while."
  • Now we have a 3D molecule in our PDF.
  • Click onto the molecule to activate it. This is what the reader will see when they open your PDF.
  • Open the molecule tree.
  • From the molecule tree you can turn on and off different nodes to make preset views by checking the boxes next to the nodes.
  • This allows the author to show readers particular areas or interactions that are important to the paper but the reader can still interact with the figure, even turn off nodes themselves.
  • Try turning off the first four nodes and save it as a preset view by clicking the camera button.
  • Turn all the nodes back on and take another picture. Call this one, "all nodes."
  • There are also preset views that automatically appear when you import a 3D object. They are all the same distance from the "camera" and contain all the nodes.
  • As you can see, additional tools are available within Adobe to further enhance your presentation. You can find information on the more advanced features in the Adobe documentation.