MolviZ.Org

Molecular Visualization Resources
all free and open source,
collected by Eric Martz
,
including all Martz-authored molecular visualization projects.


Interactive Tutorials & Tools in
JSmol   and   Jmol

Atlas of Macromolecules
FirstGlance in Jmol   •   Site Map
What's ?
       
Tutorials, most coauthored by Eric Martz.
    Free, Interactive Tutorials in Jmol:

 JSmol  tutorials run immediately on computers, iPads, smart phones.
  • Windows (Chrome or Firefox recommended. Internet Explorer is too slow with JSmo!)
  • Mac OSX (Safari or Chrome recommended)
 Jmol  tutorials require Java:
   INSTRUCTIONS FOR ENABLING UNSIGNED JAVA APPLETS.

DNA Structure JSmol
An introductory level, nonlinear self-paced tutorial.

(Español - Português - Deutsch - français - others)

Hemoglobin Jmol
An introductory presentation suitable for lectures or individual study.

Antibody Jmol
An introductory presentation suitable for lectures or individual study.

Major Histo- compatibility Complex Jmol
The Major Histocompatibility Complex presents peptides from foreign proteins to T lymphocytes, crucial to disease immunity.

Lipid Bilayers and Membrane Channel JSmol or Jmol
Introduces cholesterol and phospholipids, then proceeds to lipid bilayer and the gramicidin membrane channel embedded within the bilayer. Includes molecular dynamics simulations of both gel and fluid membrane states. By Eric Martz and Angel Herráez.

(Español)

Collagen JSmol
The indispensible and inextensible fibers that hold you together, by Karl Oberholser. Collagen at Wikipedia has external links to animations of collagen assembly.
Water Jmol
See 10 water molecules condense into a hydrogen-bonded droplet. Also liquid water and ice. Includes challenge questions for students. By Eric Martz and Angel Herráez.
(Español)
Lac Repressor JSmol
See how the repressor protein recognizes the DNA sequence of the lactose operator.
• Would you like to teach your students easy-to-use, state-of-the-art interactive 3D molecular visualization tools that they can expect to use for years to come?

• Would you like to use such tools yourself in your research?

Check out the
MolviZ Top 5!


Powerpoint-ready animation made with Polyview-3D. Easy enough for students!
  Other Jmol resources include:

  • Carbohydrates, lipids, vitamins, proteins, and nucleic acids in JSmol / Jmol in English or español, thanks to BioModel by Angel Herráez.
  • Proteopedia.Org JSmol: Many excellent tutorials, and it is the easiest place to create and share customized molecular scenes, or molecular structure tutorials. Easy enough for student reports or homework assignments! See teaching strategies.
  • (Jmol, for Lehninger Principles of Biochemistry) includes excellent tutorials in Jmol on
    • Protein Architecture
    • Bacteriorhodopsin
    • Lac Repressor
    • Nucleotides
    • MHC Molecules
    • Trimeric G Proteins
    • Oxygen-Binding Proteins
    • Restriction Endonucleases
    • Hammerhead Ribozyme
  • High School Biology Collection: BioMolecular Explorer 3D Jmol
  • Atlas of Macromolecules JSmol
  • Explore any molecule with FirstGlance in Jmol JSmol
  • Color proteins by evolutionary conservation, automatically, at ConSurf JSmol
  • Create publication-quality figures, and animations ready to drop into Powerpoint at Polyview-3D. Easy enough for student reports or homework assignments!
  • The Jmol Wiki has a list of Websites Using Jmol (at Jmol.Org).

Author Your Own Jmol Tutorials Easily at Proteopedia.Org! JSmol The Scene Authoring Tool there makes it easy to customize molecular views in Jmol. You don't need to learn any script, HTML, or other languages. Your descriptions and molecular scenes will be online immediately! See Comparisons. Periodic Table of the Elements Jmol
Van der Waals, uncharged, and ionic radii. Atoms sizes proportional to relative abundance in humans.
(Español)

 

What is MolviZ.Org?

MolviZ.Org brings together molecular visualization resources that Eric Martz has authored, coauthored, or recommends. These include interactive tutorials, software for molecular exploration, an Atlas with images and descriptions of selected macromolecules, physical teaching props, and more.

Types of Resources at MolviZ.Org


Site Map: MolviZ.Org

MolviZ.Org
     What is MolviZ.Org?
     Types of Resources at MolviZ.Org
     What's at MolviZ.Org?

Interactive Molecular Tutorial Collections
     Tutorials at MolviZ.Org
     Tutorials at Proteopedia, Lehninger, Biomodel
     The High School Biology Collection
     The Atlas of Macromolecules

Molecular Exploration Tools
     FirstGlance.Jmol.Org
     ConSurf Server: see evolutionary conservation.
     Proteopedia.Org

Fantastic Teaching Props
     Toobers - Model Any Type of Polymer
     Physical Molecular Models
     Physical Model Lending Library (Western MA only)

Related Resources
     Publication-Quality Figures/Animated Slides Made Easy
     A History of Visualization of Macromolecules
     Knots in Proteins
     Thermal Motion of An Alpha Helix

Interactive Molecular Tutorial Collections

Ready-To-Use Tutorials

High School Teachers' Resources

HighSchool.MolviZ.Org includes interactive molecules selected for high school curricula, alphabet traits fingerprinting, instructions for making DNA earrings, instructions for making molecules from balloons, and much more.

BioMolecular Explorer 3D (Jmol) is a collection of 3D-interactive, biologically significant molecules relevant to a high school biology curriculum. Designed by Frieda S. Reichsman, the site simplifies finding, preparing for, and using molecular visualization resources at the high school level. Includes:
  • Pre-selected molecules with descriptions to place them in context.
  • DNA, antibody, HIV protease with inhibitor, hemoglobin, lipid bilayers and channels, and more.
  • Introductions to structures of carbohydrates, lipids, vitamins, proteins and nucleic acids from BioModel by Angel Herráez.
  • Resources for lesson planning.
  • Both English and español versions of guided tutorials on DNA, carbohydrates, lipids/bilayers/channels, vitamins, proteins, and nucleic acids.

Atlas of Macromolecules JSmol

DNA Recombination (Holliday Junction). Drill for puncturing bacteria used by T4 virus. The Atlas of Macromolecules is extensively illustrated. Every entry in the Atlas can be displayed in FirstGlance in Jmol, and many in Proteopedia (neither of which require Java).

Organized by categories including enzymes, structural proteins, calcium-binding proteins, lipid bilayers, integral membrane proteins, myristoylated proteins, DNA, RNA, virus capsids, toxins, carbohydrates, magnificent molecular machines, unusual tertiary/quaternary structures, etc.



Molecular Exploration Tools

FirstGlance in Jmol (firstglance.jmol.org) JSmol

FirstGlance in Jmol (firstglance.jmol.org) enables you to explore any molecule using menus and buttons, without learning any commands, and with nothing to install (Java is optional). It works immediately with all popular browsers and computer types including recent iPads and smart phones, and is used for the 3D View links in the journal Nature, among others.

FirstGlance in Jmol offers numerous one-click preset views, makes it easy to hide portions of the molecule, find residues by sequence or name, show all protein disulfide bonds, salt bridges and cation-pi orbital interactions. Its Contacts.. dialog shows non-covalent bonds to any target moiety that you select by clicking, dividing them into seven categories that you can hide or display with checkboxes.

ConSurf output: functional variability of the peptide-binding groove of MHC I is displayed in 3D in Protein Explorer.

ConSurf Server (consurf.tau.ac.il) JSmol

See evolutionary conservation! Introduction to Evolutionary Conservation.

ConSurf makes it easy for you to identify functional regions of proteins. Each amino acid is colored by evolutionary conservation, thereby revealing conserved or highly variable patches. Results may be displayed in FirstGlance in Jmol or other viewers.

Given a 3D model or PDB code this user-friendly tool finds related protein sequences, performs multiple sequence alignments, constructs a phylogenetic tree, and assigns a conservation level 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.


Fantastic Teaching Props

Toobers in Science Education: Model Your Favorite Polymer

Toobers are inexpensive, easy to bend, foam-covered rods that hold the shapes you give them, over and over again!

They are very useful in illustrating macromolecular structure concepts. Great for all levels of science from K-12 to undergraduate. We feature several examples and also short movies to illustrate their use.



Physical Models of Molecules

Colorful, accurate models featuring embedded magnets to simulate hydrogen bonding, at varying prices—kits for water, for assembling DNA from nucleotides (image at right), and other molecules. Available for purchase from 3DMolecularDesigns.com; several available to local teachers through the Physical Model Lending Library (Western MA USA only). For information on how high-precision models are made, see the Rapid Prototyping section of History of Visualization of Biological Macromolecules.



Physical Model Lending Library (Western MA only)

More than 10 different models are available for short-term loan (about 10 days) to teachers in Western Massachusetts, including:

  • Anthrax protective antigen heptamer
  • Antibody bound to lysozyme antigen
  • DNA double helix
  • Green fluorescent protein
  • The nucleosome
  • Transfer RNA
  • Water with NaCl, EtOH, Ethane

To reserve models, and for more information, see the Lending Library for Physical Molecular Models for Western Massachusetts, USA.


Related Resources

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

Make Publication-Quality Molecular Images and Rotating Powerpoint Slides Easily!



History of Visualization of Biological Macromolecules

The History of Visualization of Biological Macromolecules answers questions such as, Where did MDL Chime come from? What about Fred's Folly and Byron's Bender? See early computer images, physical models including the latest by computer-driven laser-powered rapid-prototype engineering, and the latest molecular sculpture.


Knots in Proteins!

Are protein chains ever knotted? It's rare but it does happen—
get a good look at some Knots in Proteins!.


Alpha Helix Thermal Motion

Raul E. Cachau provided this Demonstration of Alpha Helix Thermal Motion as an example of a molecular dynamic simulation of thermal motion. Further information is available at Henry Rzepa and Benjamin Whitaker's Hyperactive Molecules Section 2.
 

Click the count above for graphs of visiting rates, browsers, operating systems, etc.


Thanks to Frieda S. Reichsman (MoleculesInMotion.Com) for improving the organization and design of this site in 2005, and for subsequent insightful feedback.

Feedback to Eric Martz
(Previous version of this page)