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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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Scientific technical presentation structure visualization with marvinspace l.jpg

Scientific & technical presentationStructure Visualization with MarvinSpace

Oct2006


Description of marvinspace l.jpg

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


Features of marvinspace l.jpg

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)


Features of marvinspace4 l.jpg

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


High quality rendering i l.jpg

High quality rendering I

  • Three different rendering quality levels

  • Line anti-aliasing and full screen option for smooth polygon edges


High quality rendering ii l.jpg

High quality rendering II

  • Optional and customizable depth cue and clipping planes

  • Near and far position setting for both


Molecule representation i l.jpg

Molecule representation I

  • wire, ball, stick, spacefill and combinations

  • dotted, mesh, solid, transparent drawing types


Molecule representation ii l.jpg

Molecule representation II


Molecular surfaces i l.jpg

Molecular surfaces I

  • Smooth and accurate surfaces

  • Various surface types: van der Waals, Connolly, solvent accessible, blobby surfaces


Molecular surfaces ii l.jpg

Molecular surfaces II


Triangle count reduction l.jpg

Triangle count reduction

  • Slightly slower surface generation – Much faster rendering

  • Geometric algorithm that preserves surface characteristics


Surface transparency l.jpg

Surface transparency


Property mapping i l.jpg

Property mapping I

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


Property mapping ii l.jpg

Property mapping II

  • Mapping custom calculated properties

  • Fully customizable display via API


Property mapping iii l.jpg

Property mapping III

  • Volumetric data, e.g. Gaussian Cube surface and property files

  • Interactive change of isosurface threshold value


Property mapping iv l.jpg

Property Mapping IV

  • Charmm PDB and grid support


Large structures l.jpg

Large structures


Large structures18 l.jpg

Large structures


Secondary structure representation i l.jpg

Secondary structure representation I


Secondary structure representation ii l.jpg

Secondary structure representation II

  • Various types: wire, trace, tube, ribbon, cartoon, etc.

  • Various colors: residue, chain, structure, rainbow, b-factor

  • Customizable


Ligand binding l.jpg

Ligand binding

  • Flexible tool for binding studies


Labels l.jpg

Labels

  • Built-in label types: atom, residue, secondary structrure, molecule

  • Customizable types, colors

  • Labels can be dragged and edited


Measurement l.jpg

Measurement

  • Distance, Bond angle, Dihedral angle

  • Interactive torsion tweak


Pharmacophore modeling l.jpg

Pharmacophore modeling


Future plans l.jpg

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


Summary l.jpg

Summary

  • 100% java (application, applet)

  • High quality rendering

  • Fast, hardware accelerated graphics

  • Programmable (API)


Slide27 l.jpg

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