MolviZ "Top 5"
The "Top 5" 3D Molecular Visualization Technologies
    for the rest of us...

... (those of us who do not solve protein 3D structures)

I. Tutorials  •  II. Tutorial-Authoring Systems  •  III. Explore Any Molecule  •  IV. See Protein Evolution  • 
V. Animate Molecules in Powerpoint
collected by Eric Martz for

  • Tutorials show you how the 3D structures of DNA, hemoglobin, and many other macromolecules support their functions.

  • Find and explore the 3D structure of any macromolecule easily.

  • Identify the parts of any 3D protein molecule whose mutations are lost from the gene pool, because they must be conserved in order to perform crucial functions.

  • Easily make 3D macromolecules rotate in your Powerpoint® slides.
  • Project the following resources in lectures, offer them to your students, or assign them.
  • Some resources are targeted specifically to high school level; (see HighSchool.MolviZ.Org); most are suitable for college and graduate levels.
  • Ready-made Tutorials on 3D structures of DNA, hemoglobin, lipid bilayers, water, and many other macromolecules.
  • Some tutorials include challenge questions (answers on request).

  • Customize interactive molecular views easily to show in class, and for your students to rotate, zoom, and admire.

  • Find and explore the 3D structure of any macromolecule easily.
  • Identify the parts of any 3D protein molecule whose mutations are lost from the gene pool (because they must be conserved [see Gallery] in order to perform its functions) or most rapidly (to support function, e.g. escape of influenza hemagglutinin from immunity.
  • Easily make 3D macromolecules rotate in your Powerpoint® slides, and your students can do the same.
  • Find and explore the key structural features of any macromolecule, easily.
  • Locate the positions of crucial residues or sequences.
  • See noncovalent bonds between any moiety and the remainder of the structure.

  • Annotate interactive macromolecular structures, without learning scripting languages, for journal supplementary materials or your lab group's website at Proteopedia.Org, a free structural biology wiki with scene-authoring tools.

  • Identify functional regions by coloring amino acids with their levels of evolutionary conservation -- in minutes, totally automatically if you wish. Locate conserved residues, e.g. for functional mutagenesis studies.
  • Make publication-quality molecular figures with ease, highlighting specific residues or regions, and customizing rendering and colors.
  • Easily make 3D macromolecules rotate/animate in your Powerpoint® slides.
  • Use state-of-the-art interactive 3D molecular visualization tools that you can expect to have available for years to come.
  • These are the easiest to use tools available.
  • All technologies on this page are free!
  • No installation is needed. Nothing to download. They just work immediately in your web browser!
  • Work on all popular computers: MS Windows, Mac OS X, linux.
  • Work in the most popular web browsers: Chrome, Safari, Firefox.

JSmol (NO Java needed) is employed by most of the sites that best meet the above goals.

I. Tutorials with interactive, mouse-rotatable molecular views:
  • MolviZ.Org has Jmol-based tutorials on DNA* double helix, hemoglobin, antibody, collagen, lac repressor*, major histocompatibility proteins*, lipid bilayers and channels, water*, and more.
    * These tutorials have challenge questions, some with lesson plans.
  • Other websites with extensive ready-made tutorials on specific molecules.
II. Jmol Tutorial-Authoring Systems

Create your own tutorials easily at Proteopedia.Org, a wiki with Scene Authoring Tools. You don't need to learn any script, HTML, or other languages. Your descriptions and molecular scenes will be online immediately! See Getting Started Authoring in Proteopedia.

Jmol Tutorial-Authoring Template (JTAT) Caution: Not yet upgraded to use JSmol (no Java). Upgrade expected sometime in 2018. Download a template for building tutorials that will display in a web browser. Supports multiple chapters and views comparing 2, 3, or 4 molecules side by side (with synchronization of mouse-directed rotations or zooms). Your tutorial will include a slider for zooming (or slabbing), spin toggle and centering buttons, details that display only when requested, and "How To" put views in Powerpoint slides, etc.

Considerably more challenging to use than Proteopedia, but you have more control and the product tutorial is more user friendly. The tutorial must be uploaded to a server to provide online access, or the tutorial can be shown offline. See the JTAT Demonstration Tutorial and tutorials on several molecules.

See Comparisons of these and other Jmol tutorial-authoring systems.
III. Explore Any Molecule
    FirstGlance in Jmol (
  • Easy enough for students, but powerful enough for researchers.
  • One-click each to see secondary structure, ligands, water, hydrophobic vs. hydrophilic, charge, disulfide bonds, salt bridges, cation-pi interactions.
  • Color keys, help, tool tips appear automatically.
  • Highlights missing residues and interprets model reliability. Explains crystallographic disorder and Rfree.
  • Shows the biological unit (functional assembly).
  • Locate amino acids or nucleotides by name, sequence, or sequence numbers.
  • Isolate any chain, ligand, range of residues, etc. by clicking on them.
  • Hide any chain, residue, or atom by clicking on it.
  • See the noncovalent interactions with any moiety you designate (by clicking on it), divided into seven categories (hydrogen bonds, van der Waals, etc.).
  • Adopted by the journal Nature (see their buttons), among others.
  • More..     Paste animated molecular scenes into Powerpoint®

  • Find Molecules To Explore:
  • Browse the Atlas of Macromolecules, which lists over 150 macromolecules, many shown in snapshots. Links are provided within the Atlas to explore each in FirstGlance in Jmol.
  • Search
    • Easiest: from the amino acid sequence in UniProt.Org - Instructions.
    • Search in OCA, which has direct links to FirstGlance in Jmol.
    • Advanced Search at the US Protein Data Bank Harder to use, though more powerful. Instructions. Lacks a direct link to FirstGlance in Jmol, so write down the 4 character PDB identification codes for molecules of interest to give to FirstGlance.
  • No empirical structure? Create a Homology Model using this Practical Guide.

  • Proteopedia.Org
  • Has a resource-rich page for every published macromolecule (>100,000). New pages added weekly.
  • Create customized molecular views easily with the built-in Scene Authoring Tools. See Getting Started Authoring in Proteopedia.
Conservation of the catalytic gorge in an enzyme (enolase, 4enl) determined by Consurf.

Animation (Powerpoint-ready) made by FirstGlance in Jmol.
IV. See Protein Evolution with the easy-to-use ConSurf Server. Comparing amino acid sequences in a family of proteins reveals highly conserved residues (or highly variable, think influenza). Evolutionary conservation of a patch of residues identifies it as supporting or performing a crucial function.

Introduction to Evolutionary Conservation.

Just specify a PDB identification code and the name of one chain, and the rest is completely automatic! Functional patches of highly conserved (or highly variable) residues can be visualized easily using FirstGlance in Jmol, which is integrated into ConSurf.

ConSurf finds protein sequences related to your 3D structure, performs multiple sequence alignments, constructs a phylogenetic tree, and assigns a conservation level (and confidence interval) to each amino acid, all automatically! Optionally, you can select the sequences and upload your own multiple sequence alignment, which will be used by ConSurf's state-of-the-art algorithms, all of which are published in peer-reviewed journals.
Nicotine (darker molecule at left) bound to nicotinic receptor (detail of 1uw6). At bottom is a cation-pi interaction critical in nicotine addiction, responsible for millions of deaths annually.

Animation (Powerpoint-ready) made by FirstGlance in Jmol. See other animation examples.
V. Animate Molecules in Powerpoint.
Print Publication-Quality Molecular Views.
Easy Enough for Students Assignments!

FirstGlance in Jmol is the easiest way to make high quality images and presentation-ready animations. See Examples. However, FirstGlance does not support customization of colors and rendering in the molecular view. Also the images generated by Jmol in FirstGlance are not quite as high quality as those generated by PyMOL.

Polyview-3D generates its images and animations at truly publication quality using PyMOL. Furthermore, it supports full customization of the molecular view.

Animation made with Polyview-3D. Larger samples and more information...

Thanks to Frieda Reichsman (MoleculesInMotion.Com) for improving the organization of this page, and for suggesting the name "Top 5".

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