- Recommended*: (easiest yet powerful; work in Windows, Mac OS X, linux; nothing to install)
Proteopedia.Org is the best place to start:
- 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.
- Top5.MolviZ.Org lists the easiest-to-use, free resources.
- 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.
- Protein Explorer in Jmol
- 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.
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