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Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.

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Presentation on theme: "Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006."— Presentation transcript:

1 Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006

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


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 other technical presentations MarvinSketch/View MarvinSpace Calculator Plugins JChem Base JChem Cartridge Standardizer Screen JKlustor Fragmenter Reactor

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