1 / 27

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

Anita
Download Presentation

Scientific & technical presentation Structure Visualization with MarvinSpace

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  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

More Related