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)
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 -
(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
Customized Molecular Scenes
are created most easily, by far, in the protein structure wiki
- 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
- MDL Chime has been eliminated from this version.
- Use with some caution as it is under development (2010) and occasional
bugs may remain.
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
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
Educational molecular visualization resources for teachers:
For high school (secondary school) biology teachers:
(New in 2009)
*Opinions and recommendations expressed on this page are those of
Last updated September, 2010