scientific technical presentation structure visualization with marvinspace
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Scientific & technical presentation Structure Visualization with MarvinSpace

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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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Presentation Transcript
description of marvinspace
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
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
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
High quality rendering I
  • Three different rendering quality levels
  • Line anti-aliasing and full screen option for smooth polygon edges
high quality rendering ii
High quality rendering II
  • Optional and customizable depth cue and clipping planes
  • Near and far position setting for both
molecule representation i
Molecule representation I
  • wire, ball, stick, spacefill and combinations
  • dotted, mesh, solid, transparent drawing types
molecular surfaces i
Molecular surfaces I
  • Smooth and accurate surfaces
  • Various surface types: van der Waals, Connolly, solvent accessible, blobby surfaces
triangle count reduction
Triangle count reduction
  • Slightly slower surface generation – Much faster rendering
  • Geometric algorithm that preserves surface characteristics
property mapping i
Property mapping I
  • Built-in surface coloring options: atom types, residue, chain id, B-factor secondary structure, electrostatic potential
property mapping ii
Property mapping II
  • Mapping custom calculated properties
  • Fully customizable display via API
property mapping iii
Property mapping III
  • Volumetric data, e.g. Gaussian Cube surface and property files
  • Interactive change of isosurface threshold value
property mapping iv
Property Mapping IV
  • Charmm PDB and grid support
secondary structure representation ii
Secondary structure representation II
  • Various types: wire, trace, tube, ribbon, cartoon, etc.
  • Various colors: residue, chain, structure, rainbow, b-factor
  • Customizable
ligand binding
Ligand binding
  • Flexible tool for binding studies
  • Built-in label types: atom, residue, secondary structrure, molecule
  • Customizable types, colors
  • Labels can be dragged and edited
  • Distance, Bond angle, Dihedral angle
  • Interactive torsion tweak
future plans
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
  • 100% java (application, applet)
  • High quality rendering
  • Fast, hardware accelerated graphics
  • Programmable (API)

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