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Scientific & technical presentation Structure Visualization with MarvinSpace

Scientific & technical presentation Structure Visualization with MarvinSpace. Oct 200 6. Description of MarvinSpace. high performance 3D molecule visualization tool WEB enabled, platform independent available as standalone application with an easy-to-use GUI Java Applet

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Scientific & technical presentation Structure Visualization with MarvinSpace

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  1. Scientific & technical presentationStructure Visualization with MarvinSpace Oct2006

  2. Description of MarvinSpace • high performance 3D molecule visualization tool • WEB enabled, platform independent • available as • standalone application with an easy-to-use GUI • Java Applet • developers' toolkit • visualizes • small molecules, proteins, nucleic acids, crystals, • molecular surfaces, molecular orbitals, volumetric data

  3. Features of MarvinSpace Key features of v5.0 • pure java (all platforms, html integration, applet) • programmable (via java API) • scalable rendering quality • high quality image capturing • accurate surface representation including Connolly • property mapping on surface (e.g. electrostatic potential) • extendable (custom components, calculations can be integrated) • professional support (24 hour response time, rapid implementation of feature requests etc)

  4. Features of MarvinSpace Other features of v5.0 • table view (multiple cells) • multiple molecule view (overlayed ligands; show/hide, add/remove) • ball, stick, spacefill; cartoon representation • dynamic surface coloring, transparency • distance and angle measurement; change of conformation about rotatable bonds • high quality rendering (depth cueing, perspective projection, anti-aliasing) • clipping • atom, bond, residue, molecule, surface component picking

  5. High quality rendering I • Three different rendering quality levels • Line anti-aliasing and full screen option for smooth polygon edges

  6. High quality rendering II • Optional and customizable depth cue and clipping planes • Near and far position setting for both

  7. Molecule representation I • wire, ball, stick, spacefill and combinations • dotted, mesh, solid, transparent drawing types

  8. Molecule representation II

  9. Molecular surfaces I • Smooth and accurate surfaces • Various surface types: van der Waals, Connolly, solvent accessible, blobby surfaces

  10. Molecular surfaces II

  11. Triangle count reduction • Slightly slower surface generation – Much faster rendering • Geometric algorithm that preserves surface characteristics

  12. Surface transparency

  13. Property mapping I • Built-in surface coloring options: atom types, residue, chain id, B-factor secondary structure, electrostatic potential

  14. Property mapping II • Mapping custom calculated properties • Fully customizable display via API

  15. Property mapping III • Volumetric data, e.g. Gaussian Cube surface and property files • Interactive change of isosurface threshold value

  16. Property Mapping IV • Charmm PDB and grid support

  17. Large structures

  18. Large structures

  19. Secondary structure representation I

  20. Secondary structure representation II • Various types: wire, trace, tube, ribbon, cartoon, etc. • Various colors: residue, chain, structure, rainbow, b-factor • Customizable

  21. Ligand binding • Flexible tool for binding studies

  22. Labels • Built-in label types: atom, residue, secondary structrure, molecule • Customizable types, colors • Labels can be dragged and edited

  23. Measurement • Distance, Bond angle, Dihedral angle • Interactive torsion tweak

  24. Pharmacophore modeling

  25. Future plans • scripting (Chime) • live content, presentation support • more property calculations (e.g. hydrophobic areas, electron density) • detection of interaction sites • perception and visualization of hydrogen bonds • interactive molecule construction • stereo view • volume rendering • navigation bar • 3d overlay, pharmacophore modeling • share molecular information by labeling and annotating atoms, bonds, ligands, receptors, complexes, surface regions • protein-ligand binding energy calculation, scoring, boundary clash

  26. Summary • 100% java (application, applet) • High quality rendering • Fast, hardware accelerated graphics • Programmable (API)

  27. Visit othertechnical presentations MarvinSketch/Viewhttp://www.chemaxon.com/MarvinSketch_View.ppt MarvinSpacehttp://www.chemaxon.com/MarvinSpace.ppt Calculator Pluginshttp://www.chemaxon.com/Calculator_Plugins.ppt JChem Basehttp://www.chemaxon.com/JChem_Base.ppt JChem Cartridgehttp://www.chemaxon.com/JChem_Cartridge.ppt Standardizerhttp://www.chemaxon.com/Standardizer.ppt Screenhttp://www.chemaxon.com/Screen.ppt JKlustorhttp://www.chemaxon.com/JKlustor.ppt Fragmenterhttp://www.chemaxon.com/Fragmenter.ppt Reactor http://www.chemaxon.com/Reactor.ppt

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