Monolith: Collaborative Molecular Visualization for Second Life

Monolith is a molecular visualization system created to display molecular structures within the virtual world known as Second Life and allow real-time interaction with the displayed structures.  By bringing molecular visualization within Second Life, analysis and learning of molecular structure becomes a highly collaborative process in which participants can be in distant locations throughout the world viewing the same structure at the same time.  Real-time voice and instant messaging, provided by Second Life, allow for students and researchers to share their ideas.

The three dimensional nature of Second Life makes for a perfect environment for displaying true three dimensional information.

Monolith currently has the ability to load structures from the RCSB Protein Data Bank but will also incorporate other datasources in the near future such as loading pdb structural files from arbitrary web sites.

Main features:

  • Ability to load any structure within the RCSB Protein Data Bank (more sources in future versions of Monolith)
  • Rapid rez rates (>3200 atoms in 55 seconds)
  • Ability to change color on any atom(s) interactively based on residue #, residue name, and atom element type
  • Ability to set labels over any atom
  • Ability to change transparency (alpha) from opaque to invisible
  • Ability to display only a subset of atoms and then also display in addition atoms that are a specified distance from those selected atoms