MarvinSpace

Overview

MarvinSpace is a high performance 3D molecule visualization tool available on a range of platforms including Windows, Linux, Mac OS X, and Solaris.

MarvinSpace is WEB enabled, its seamless integration in html pages makes it an ideal platform independent and cross-platform molecule visualizer. It is available as a standalone application with an easy-to-use GUI, as a Java Applet and also as a developers’ toolkit that provides full-featured Application Programming Interface to support easy integration in custom applications.

Using MarvinSpace you can visualize small molecules, proteins, nucleic acids, crystals, various molecular surfaces, molecular orbitals as well as volumetric data such as electrostatic potential, hydrophobicity. Manual overlay of structures and manual change of internal coordinates are also available.

Beyond visualization MarvinSpace allows you to share molecular information by labeling and annotating atoms, bonds, ligands, receptors, complexes, surface regions.

3D visualization of molecules

• Draw types: wireframe, ball, stick, spacefill
• Color modes: cpk, residue, chain, constant
• Labels: atom labels, residue labels, secondary structure label, editable labels, label coloring
• Property settings: radii, colors, color schemas, controls keys, mouse control

Enhanced visualization

• Optional depth cue, interactive control of fog start and fog end
• Clipping planes, interactive translation of near and far clipping planes
• Line and poligon anti-aliasing

3D manipulation

• Scene: rotation, translation and zoom
• Component: translation, rotation, scaling
• Individual component selection, hide, show, delete, fade
• Multiple cell view, synchronuous transformations of cells

Monitors and controls

• Geometry measurements: distances, bond angle, dihedral angle
• Controls: translate, rotate molecules individually, change dihedral angle interactively
• All monitors are refreshed while components or controls are being changed

Macromolecules

• Component recognition and classification: chains, ligands, ions, water molecules
• Easy access to individual components
• Secondary structure visualization (cartoon, ribbon) and coloring

Molecular surfaces

• Various surface types: van der Waals, solvent accessible, Connolly surface; blobby surface
• Fast surface calculation, accurate representation
• Several display modes: dotted, mesh, filled, transparent
• Coloring: by atom type, residue type, chain type, B-factor and other atomic properties; electrostatic potential and other volumetric data
• customizable property mapping, property interpolation, property superposition, color blending
• Iso surfaces, interactive cut-off

Details

MarvinSpace is a Java-based 3-dimensional molecular structure visualization program. Its main purpose is to display macromolecules including proteins, nucleic acids, and protein-ligand complexes. MarvinSpace is an interactive program, which means that it does not merely display a static image but it allows the user to manipulate the structure: look at it from different aspects, various distances, look inside etc. MarvinSpace can also be used to display and manipulate small molecules, particularly if high quality rendering is required.
MarvinSpace is built on OpenGL, the industry standard 3D visualization language to render high quality molecular scenes. Beside high image quality, OpenGL also provides efficiency that allows real-time manipulation of molecular structures. OpenGL supports hardware acceleration, that is, it can fully exploit the capabilities of the particular graphics card being used.

FAQ

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