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Towards Interactive 3D Graphics in Chemistry Publications

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Presentation at the MM2009, Gold Coast, Queensland, Australia

Presentation at the MM2009, Gold Coast, Queensland, Australia

Published in Education , Technology
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  • 1. Towards Interactive 3D Graphics in Chemistry Publications Vladislav Vasilyev Supercomputer Facility Australian National University, Canberra, Australia
  • 2. Computational Chemistry is Dealing with Intristically 3-Dimensional Data
    • There are plenty of molecular-visualization programs, both freeware and commercial ones, which can provide interactive representations of molecular geometry and 3D properties
  • 3. Publication of Calculated Results is Limited to the Static 2-Dimensional (2D) Images
    • Although many scientific publishers allow linking of supplementary materials to the original articles, it could require readers to have dedicated visualization software, (format conversion) tools, etc.
    • Thus the effective communication between the authors and readers is limited.
  • 4. Possible Solution?
    • The use of publishing technology which embeds the 3D information into the original paper
    • 3D information should be accessed by all readers interactively without the need for any additional software
  • 5. PDF is Current Gold Standard of Electronic Publishing
  • 6. Dealing with 3D Data in PDF Traditional Approach
    • Showing 3D Data as 2-Dimensional Pictures
    • Linking suplementary material from published papers
    • -> need for specialized visualization software, tools, etc.
  • 7. Dealing with 3D Data in PDF 3d Approach
    • Starting from the Adobe Acrobat 7.0 family in 2005 it has became possible to embed, view, and navigate 3D content in PDF files.
    • The embedded 3D content can be viewed and fully interacted with the free Adobe Acrobat Reader on any computer, with no additional visualization software required
  • 8. How to Embed 3D Data into PDF Only Acrobat 9 Pro Extended can be used for creating 3D PDF Documents
  • 9. For the LaTeX Geeks…
    • movie15
    • http://www.ctan.org/tex-archive/macros/latex/contrib/movie15/
    • movie15 package provides an interface to embed movies, sounds and 3D objects into PDF documents for use with LaTeX as well as pdfLaTeX .
  • 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
  • 14. 2) Inserting 3D Object in Acrobat 9 Pro Extended: Capturing 3D Scene
    • Acrobat captures a 3D model from any 3D CAD application that supports OpenGL.
    • The 3D capture is not that straightforward and requires specific settings for different applications in order to work.
  • 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
  • 18. Embedding the Dynamic 3D Content into Adobe PDF Using JavaScript
    • Adobe Acrobat can provide far more capabilities than a simple document viewer
    • PDF document can contain elements of the Graphical User Interface (GUI) such as buttons, checkboxes, combo boxes, etc. to initiate user actions
    • This can be achieved using the Acrobat JavaScript
  • 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)
  • 22. How to Embed Molecules and 3D Molecular Properties into 3D PDF?
    • 27 Computer-Aided Design formats
    • Screen capture
    • VMD -> Screen Capture
    • PyMol -> VRML file
    • Jamberoo (former JMolEditor) -> VRML
  • 23. General Workflow Using VRML 3D Scene
    • Virtual Reality Modeling Language (VRML) File
    • VRML is an ASCII (text) file format
    • It can be visualized by VRML viewers and can be edited in text or VRML editors
    • Thus, the VRML format gives more control over the 3D scene for advanced users.
    3D PDF
  • 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 PBD 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
  • 39. Acknowledgments
    • Prof. Feng Wang and Dr. David G. Barnes (Swinburne University of Technology, Melbourne) for bringing 3D PDF capabilities to my attention and useful discussions
    • Dr. Kevin Pulo – Supercomputer Facility, ANU