The document discusses embedding interactive 3D graphics in chemistry publications using PDF format. It describes how 3D molecular structures and properties can be inserted into PDFs using programs like Acrobat and Jamberoo. Readers can then interact with these 3D objects directly in the PDF without additional software. The document provides tutorials and examples of inserting 3D content from various file formats and chemistry programs into PDFs.

1. Towards Interactive 3D Graphics in Chemistry Publications Vladislav Vasilyev Supercomputer Facility Australian National University, Canberra, Australia

5. PDF is Current Gold Standard of Electronic Publishing

8. How to Embed 3D Data into PDF Only Acrobat 9 Pro Extended can be used for creating 3D PDF Documents

10. Inserting 3D Object in Acrobat 9 Pro Extended

11. 1) Inserting 3D Object in Acrobat 9 Pro Extended: Loading CAD * File * CAD – Computer-Aided Design

12. 3D PDF and Microsoft Office products Word, PowerPoint, and Excel In Microsoft Office applications, user can adjust the placement, background color, and other properties of inserted 3D models (hide or isolate parts, create new views, and set model perspective). The resulted Office document with the embedded 3D model(s) can be converted into the 3D PDF.

13. 3D PDF Object in PowerPoint

15. Custom Views in 3D PDF Custom Views help readers to navigate quickly the 3D content (such as top, bottom, left, right, inside, outside, etc.).

16. Custom Views in 3D PDF Custom Views help readers to navigate quickly the 3D content: molecule, molecule+ESP, molecule+HOMO, molecule+LUMO

17. Poster Image in 3D PDF 2D image that is not part of the 3D content which is displayed when the interactive content is not activated. Poster Image 3D Content

19. The Dynamic 3D Content: Using Check Boxes Show/Hide Displacement Vectors Show/Hide Displacement Vectors Execute JavaScript to show/hide particular graphics nodes

20. The Dynamic 3D Content: Using Radio Boxes Execute JavaScript to show/hide particular graphics nodes

21. The Dynamic 3D Content: Creating Animations Execute JavaScript to show/hide particular graphics nodes (frames)

24. On-Line Tutorial for Creating 3D PDF http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/tutorials/3d-pdf/

25. On-Line Tutorial for Creating 3D PDF Step by step instructions, samples of JavaScript http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/tutorials/3d-pdf/

26. Jamberoo – Molecular Editor/Builder On the web: http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html ~8100 downloads from 77 countries for two years

27. Jamberoo Supports Many Popular Computational Chemistry Formats Gaussian GAMESS Mopac PDB Tripos Mol2 Amber Gromacs etc.

28. Molecular Builder/Editor Adding/deleting Atoms Adding Fragments Adding Molecules Modifying atoms, bonds, angles, dihedral angles Automatic filling of empty valences with hydrogens

29. Building Molecule Using Fragment Library

30. Working with System Clipboard Selection in Text Editor Gaussian Output File

31. Visualizing Volumetric Data (Gaussian cubes)

32. High quality graphics for publishing: Image Capture

33. H igh quality graphics for publishing: POV-Ray Generated by POV-Ray (The Persistence of Vision Raytracer)

34. Easy access to files on remote computers

35. Interactive Charts (MD, Optimization) ADF (output files) Gaussian (output files) VASP (vasprun.xml)

36. Displaying Vibrational Spectra Use combobox to select spectrum to plot and press “Show Spectrum” button to plot selected spectrum Implemented for Gaussian output files

37. Displaying Vibrational Modes Shows Animation of Vibrations and Displacement Vectors Implemented for Gaussian & ADF output files

38. Conclusions PDF documents with integrated 3D models provide new ways of visualizing complex molecular properties in an instructive and interactive manner which is ideally suited for the research and educational purposes