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)
    • Protein Data Bank 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.
      • 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   
      • 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.
  • Other free molecular visualization software packages are listed at MolVisIndex.Org.

Educational molecular visualization resources for teachersMolviZ.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.


As life is more than 2D, Proteopedia helps to bridge the gap between 3D structure & function of biomacromolecules. Proteopedia presents this information in a user-friendly way as a collaborative & free 3D-encyclopedia of proteins & other biomolecules.

FirstGlance in Jmol: Guided macromolecular visualization with remarkable ease of use.

MolviZ “Top 5”: The “Top 5” 3D Molecular Visualization Technologies