Judit Papp, Mikl

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Scientific technical presentationStructure
Visualization with MarvinSpace

• Judit Papp, Miklós Vargyas

May 2006
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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

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Features of MarvinSpace

• Key features of v1.3
• 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)

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Features of MarvinSpace

• Other features of v1.3
• 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

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High quality rendering I

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

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High quality rendering II

• Optional and customizable depth cue and clipping
  planes
• Near and far position setting for both

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Molecule representation I

• wire, ball, stick, spacefill and combinations
• dotted, mesh, solid, transparent drawing types

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Molecule representation II
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Molecular surfaces I

• Smooth and accurate surfaces
• Various surface types van der Waals, Connolly,
  solvent accessible, blobby surfaces

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Molecular surfaces II
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Triangle count reduction

• Slightly slower surface generation Much faster
  rendering
• Geometric algorithm that preserves surface
  characteristics

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Surface transparency
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Property mapping I

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

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Property mapping II

• Mapping custom calculated properties
• Fully customizable display via API

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Property mapping III

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

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Large structures
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Large structures
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Secondary structure representation
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Ligand binding

• Flexible tool for binding studies

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Labels

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

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Measurement

• Distance, Bond angle, Dihedral angle
• Interactive torsion tweak

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Pharmacophore modeling
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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

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Summary

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

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