towards interactive 3d graphics in chemistry publications

Towards Towards Interactive 3D Graphics Interactive 3D Graphics in in Chemistry PublicationsChemistry Publications

Vladislav VasilyevVladislav Vasilyev

Supercomputer FacilitySupercomputer Facility

Australian National University, Canberra, AustraliaAustralian National University, Canberra, Australia

Computational Chemistry is Dealing Computational Chemistry is Dealing with Intristically 3-Dimensional Datawith 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

Publication of Calculated Results is Limited Publication of Calculated Results is Limited to the Static 2-Dimensional (2D) Imagesto 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 Thus the effective communication between the authors and readers is limited.readers is limited.

Possible Solution?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

PDF PDF is Current Gold Standard of is Current Gold Standard of Electronic PublishingElectronic Publishing

Dealing with 3D Data in PDFDealing with 3D Data in PDFTraditional ApproachTraditional Approach

• Showing 3D Data as 2-Dimensional Pictures

• Linking suplementary material from published papers

→ need for specialized visualization software, tools, etc.

Dealing with 3D Data in PDFDealing with 3D Data in PDF3d Approach3d 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

How to Embed 3D Data into PDFHow to Embed 3D Data into PDF

Only Acrobat 9 Pro Extended can be used for creating 3D PDF Documents

For the LaTeX Geeks…For the LaTeX Geeks…

• movie15movie15

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.

Inserting 3D Object in Acrobat 9 Pro Inserting 3D Object in Acrobat 9 Pro ExtendedExtended

1) Inserting 3D Object in Acrobat 9 1) Inserting 3D Object in Acrobat 9 Pro Extended: Pro Extended: Loading CADLoading CAD** File File

* CAD – Computer-Aided Design* CAD – Computer-Aided Design

3D PDF and Microsoft Office products 3D PDF and Microsoft Office products

Word, PowerPoint, and ExcelWord, 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.

3D PDF Object in PowerPoint

2) Inserting 3D Object in Acrobat 9 2) Inserting 3D Object in Acrobat 9 Pro Extended: Pro Extended: Capturing 3D SceneCapturing 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.

Custom Views in 3D PDFCustom Views in 3D PDF

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

Custom Views in 3D PDFCustom Views in 3D PDF

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

Poster Image in 3D PDFPoster 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

Embedding the Dynamic 3D Content Embedding the Dynamic 3D Content into Adobe PDF Using JavaScriptinto 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

The Dynamic 3D Content: Using The Dynamic 3D Content: Using Check BoxesCheck Boxes

Show/Hide Displacement Vectors

Show/Hide Displacement Vectors

Execute JavaScript to show/hide particular graphics nodes

The Dynamic 3D Content: Using The Dynamic 3D Content: Using Radio BoxesRadio Boxes

Execute JavaScript to show/hide particular graphics nodes

The Dynamic 3D Content: Creating The Dynamic 3D Content: Creating AnimationsAnimations

Execute JavaScript to show/hide particular graphics nodes (frames)

How to Embed Molecules and 3D How to Embed Molecules and 3D Molecular Properties into 3D PDF?Molecular Properties into 3D PDF?

1) 27 Computer-Aided Design formats

2) Screen capture

• VMD → Screen Capture

• PyMol → VRML file

• Jamberoo (former Jamberoo (former JMolEditor) → VRMLJMolEditor) → VRML

General Workflow Using VRMLGeneral 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

On-Line Tutorial for Creating 3D On-Line Tutorial for Creating 3D PDFPDF

http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/tutorials/3d-pdf/

On-Line Tutorial for Creating 3D PDFOn-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/

JamberooJamberoo – Molecular Editor/Builder – 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

Jamberoo Jamberoo Supports Many Popular Supports Many Popular Computational Chemistry FormatsComputational Chemistry Formats

Gaussian

GAMESS

Mopac

PDB

Tripos Mol2

Amber

Gromacs

etc.

Molecular Builder/EditorMolecular Builder/Editor

Adding/deleting Atoms

Adding Fragments

Adding Molecules

Modifying atoms, bonds, angles, dihedral angles

Automatic filling of empty valences with hydrogens

Building Molecule Using Fragment LibraryBuilding Molecule Using Fragment Library

Working with System ClipboardWorking with System Clipboard

Selection in Text Editor

Gaussian Output File

Visualizing Volumetric Data (Gaussian cubes)Visualizing Volumetric Data (Gaussian cubes)

High quality graphics for publishing: Image CaptureHigh quality graphics for publishing: Image Capture

HHigh quality graphics for publishing: POV-Rayigh quality graphics for publishing: POV-Ray

Generated by POV-Ray (The Persistence of Vision Raytracer)

Easy access to files on remote computersEasy access to files on remote computers

Interactive Charts (MD, Optimization)Interactive Charts (MD, Optimization)

ADF (output files)ADF (output files)

Gaussian (output files)Gaussian (output files)

VASP (vasprun.xml)VASP (vasprun.xml)

Displaying Vibrational SpectraDisplaying Vibrational Spectra

Use combobox to select spectrum Use combobox to select spectrum to plot and press “Show to plot and press “Show Spectrum” button to plot selected Spectrum” button to plot selected spectrumspectrum

Implemented for Gaussian Implemented for Gaussian output filesoutput files

Displaying Vibrational ModesDisplaying Vibrational Modes

Shows Animation of Shows Animation of Vibrations and Vibrations and Displacement VectorsDisplacement Vectors

Implemented for Gaussian & Implemented for Gaussian & ADF output filesADF output files

ConclusionsConclusions

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

AcknowledgmentsAcknowledgments

• Prof. Feng WangProf. 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 PuloDr. Kevin Pulo – Supercomputer Facility, ANU