Scientific & technical presentation

Structure Visualization with

MarvinSpace

Oct 2006

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

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 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

• Three different rendering quality levels

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

High quality rendering II

• Optional and customizable depth cue and clipping planes

• Near and far position setting for both

Molecule representation I

• wire, ball, stick, spacefill and combinations

• dotted, mesh, solid, transparent drawing types

Molecule representation II

Molecular surfaces I

• Smooth and accurate surfaces

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

Molecular surfaces II

Triangle count reduction

• Slightly slower surface generation – Much faster rendering

• Geometric algorithm that preserves surface characteristics

Surface transparency

Property mapping I

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

Property mapping II

• Mapping custom calculated properties

• Fully customizable display via API

Property mapping III

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

• Interactive change of isosurface threshold value

Property Mapping IV

• Charmm PDB and grid support

Large structures

Large structures

Secondary structure representation I

Secondary structure representation II

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

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

• Customizable

Ligand binding

• Flexible tool for binding studies

Labels

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

• Customizable types, colors

• Labels can be dragged and edited

Measurement

•Distance, Bond angle, Dihedral angle

•Interactive torsion tweak

Pharmacophore modeling

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

• 100% java (application, applet)

• High quality rendering

• Fast, hardware accelerated graphics

• Programmable (API)

Visit other technical presentations

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MarvinSpace http://www.chemaxon.com/MarvinSpace.ppt

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