2010:
Options for exploring, presenting, and sharing 3D macromolecular structure models (PDB files), all free:
  • Recommended*: (easiest yet powerful; work in Windows, Mac OS X, linux; nothing to install)
    • Proteopedia.Org is the best place to start:
        For every molecule in the Protein Data Bank, it has
      • An interactive 3D view in Jmol.
      • Full names of ligands, sites, non-standard residues.
      • Color by evolutionary conservation (ConSurf) to identify functional sites.
      • Published abstract.
      • Link to FirstGlance in Jmol ...

      • Articles explaining structural bioinformatics terms and concepts including asymmetric unit, biological unit, electron density maps, NMR, resolution, R free, R value, See list at About Macromolecular Structure.
    • FirstGlance in Jmol - FirstGlance.Jmol.Org (easiest available; used by Nature et al.)
        One-click views of major structural features including:
      • Secondary structure, N and C termini
      • Composition (protein, DNA, RNA, ligands, solvent)
      • Hydrophobic vs. polar; charge
      • Non-covalent interactions with any moiety you specify
      • Find by sequence number or name; Hide portions.
      • Salt bridges, cation-pi interactions, temperature and more.
    • Customized Molecular Scenes are created most easily, by far, in the protein structure wiki
        Proteopedia.Org:
      • Scene-Authoring Tools make it easy (menus, buttons, forms; no command language to learn!)
      • See scene in Jmol as you create it (WSYWIG). Undo button!
      • Videos show you how.
      • Saved scenes are immediately on-line to share with anyone.
      • Popup button enlarges molecular scenes to full screen for lecture projection.
      • Save any page for off-line display.
      • Protect pages so only you can change them.
    • Powerpoint Slides, Publication-Quality Molecules, Animations, etc.

  • Also Excellent
    • Protein Explorer in Jmol   Jmol.ProteinExplorer.Org
      • A Jmol version of the original Protein Explorer (see below) ported and greatly enhanced by Bob Hanson.
      • MDL Chime has been eliminated from this version.
      • Use with some caution as it is under development (2010) and occasional bugs may remain.

  • Defunct
    • Protein Explorer in Chime - Caution: No Longer Supported! Works only in Windows with Firefox. Sometimes fussy to get working.
      • Must install an older version of the free MDL Chime browser plugin.
      • Make custom views with complete control over the molecular view. Undo.
      • No easy way to share customized molecular scenes (unlike Proteopedia.Org).

    • Older versions of Protein Explorer

  • Other free molecular visualization software packages are listed at MolVisIndex.Org.
Educational molecular visualization resources for teachers: MolviZ.Org
For high school (secondary school) biology teachers: HighSchool.MolviZ.Org (New in 2009)

*Opinions and recommendations expressed on this page are those of Eric Martz.
Last updated September, 2010