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
  and  
Atlas of Macromolecules
FirstGlance in Jmol   •   Protein Explorer
Site Map   •   What's ?
       
Tutorials, most coauthored by Eric Martz.
    Free, Interactive Tutorials in Jmol: Nothing* to install!
These run immediately in
  • Windows (Internet Explorer or Firefox recommended)
  • Mac OSX (Safari recommended)
  • linux (Firefox recommended)
*Windows users may need to upgrade java.     Regular Apple software updates are recommended for Mac users.

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

(Español - Português - Deutsch)

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 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 Jmol
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 Jmol
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?

• Would you like to eliminate MDL Chime?

Check out the
MolviZ Top 5!


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

To stop animations on this page hit the Esc key. To restart them, click the Refresh button on your browser.
Author Your Own Jmol Tutorials Easily at Proteopedia.Org! 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)

Free, Interactive Tutorials in MDL Chime.

Chime is an older molecular display technology than is Jmol, and has some limitations. Chime is slowly being phased out (More..). We continue to offer these because some of them have not yet been ported to Jmol, so are available only in Chime; some have more translations into other languages than the Jmol versions; and all can be be downloaded for off-line use.
  • Chime is free, but you must install Chime (and test your Chime) before you can see these tutorials -- and they work only in Windows, and only in certain browsers.
  • All Chime tutorials here work very well in Windows Firefox (recommended).
  • The tutorials marked *Win-IE6-Compatible* also work in Windows Internet Explorer 6.
  • Chime (and therefore these tutorials) do not work at all in Internet Explorer 7.
  • Chime does not work on Mac OSX, but runs in a Windows virtual machine on Intel Macs.
  • Most of the Chime resources here can be downloaded for off-line use. In contrast, the Jmol resources here work only on-line.
Tutorials in this section were authored by Eric Martz and other coauthors as noted

To stop animations on this page hit the Esc key. To restart them, click the Refresh button on your browser.

Hemoglobin Chime
An introductory presentation suitable for lectures or individual study.
(Deutsch, Português)

DNA Structure Chime
An introductory level, nonlinear self-paced tutorial. (Deutsch, Español, Português)

*Win-IE6-Compatible*

Antibody Chime
An introductory presentation suitable for lectures or individual study.
(Deutsch)

MHC Chime
The Major Histocompatibility Complex presents peptides from foreign proteins to T lymphocytes, crucial to disease immunity.

Lipid Bilayers and Membrane Channel Chime
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)

Molecular Vibrations: IR Spectrum Chime
by Motyka, Lahti & Lancashire.

*Win-IE6-Compatible*

Water Chime
Theoretical simulation of 10 water molecules condensing into a hydrogen-bonded droplet. Includes challenge questions for students.

*Win-IE6-Compatible*

Lac repressor Chime
bending the DNA operon as it goes from nonspecific to specific DNA binding.

*Win-IE6-Compatible*

Bacterial Flagellar Hook Chime
Bacterial flagella are whip-like organelles that bacteria use to swim about. The hook acts as a molecular universal joint. It's composed of over 100 protein subunits.

*Win-IE6-Compatible*

 

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, an indexed list of online tutorials by many different authors, physical teaching props, and more. MolviZ.Org resources can be used online; those using Chime can also be downloaded.

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?
     Download MolViz Resources
     Site Statistics

Interactive Molecular Tutorial Collections
     Martz-Authored Tutorials
     The High School Biology Collection
     The Atlas of Macromolecules
     The World Index of Molecular Visualization Resources

Molecular Exploration Tools
     FirstGlance.Jmol.Org
     ConSurf Server: see evolutionary conservation.
     ProteinExplorer.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
     RasMol
     Knots in Proteins
     Amino Acid Quizzer
     Thermal Motion of An Alpha Helix

Technical

Jmol
     Jmol Tutorial-Authoring Template
     Jmol.Org: Demonstrations, Documentation, Jmol Downloads

Chime is being phased out, but it will take years before most Chime resources are available in Jmol!

Chime Requirements
     Chime
     Chime-Compatible Browsers
     Operating Systems
     Test Your Chime Installation
     Troubleshooting

Chime
     About Chime
     What is Chime?
     Downloading and Installing Chime
     How to Use Chime Tutorial Controls
     How to Create Chime Tutorials
     Command Language/Reference Manuals
     Animation of XYZ Files: A Demonstration
     Frequently Asked Questions
     A History of Chime Versions

 

Interactive Molecular Tutorial Collections

Martz-Authored Tutorials in Jmol (or Chime).

Ready-to-use tutorials, listed above, with animated excerpts.

High School Biology Collection Jmol

BioMolecular Explorer 3D 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.

World Index of Molecular Visualization Resources Jmol, Chime, and others

The World Index of Molecular Visualization Resources (molvisindex.org) has hundreds of resources, fully cross-referenced! Categories include:

  • Biochemical Structure Tutorials
  • K-12 Tutorials
  • Non-English Resources
  • How to Create New Tutorials with Chime
  • Galleries of Molecular Images
  • Physical Molecular Models
  • Free Molvis Software
  • Commercial Molvis Software
  • Where to get Molecules
  • Organic Chemistry Tutorials
  • Inorganic/Crystal Tutorials
  • EMail Lists, Newsgroups

Atlas of Macromolecules Jmol and Chime

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 either FirstGlance in Jmol and in Protein Explorer (Chime, *Win-IE6-Compatible*).

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) Jmol

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. It works immediately with all popular browsers and computer types. It is designed for professionals reading journal articles (look for 3D View links in Nature Structural and Molecular Biology, among others). It has less help for students than Protein Explorer, but it is simpler to use.

FirstGlance in Jmol offers several one-click preset views, makes it easy to hide portions of the molecule, find residues by sequence number or name, show all protein salt bridges and cation-pi orbital interactions (under More Views..). 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) Jmol

See evolutionary conservation!

ConSurf makes it easy for you to identify functional regions of proteins. Each amino acid is colored by evolutionary conservation, thereby making clear conserved or highly variable patches. Results are displayed in FirstGlance in Jmol (or Protein Explorer). Results can be downloaded in a single PDB file and later uploaded to FirstGlance in Jmol for display.

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.

ProteinExplorer.Org    Chime  *Win-IE6-Compatible*    (en español)       Downloadable

Screenshot of Protein Explorer's QuickViews Menu System. With ProteinExplorer.Org you can explore any molecule, using menus and buttons without typing any commands. Makes visual exploration of macromolecular structure much more accessible to novices and research professionals alike. Easier to use and more powerful than RasMol. And, if you have used RasMol, you can enter any commands you have already learned. Includes Lesson Plans for Educators. In addition, it's downloadable for off-line use!

Reviews: Protein Explorer review by MERLOT. PE received the highest rating and won the annual MERLOT Classics Award for 2003: "Protein Explorer has revolutionized the teaching of biology at a molecular level." More reviews.

Learn how to use Protein Explorer quickly and efficiently by viewing our interactive Flash movie, Getting Started in Protein Explorer.

Make slides with rotating molecular structures! PE makes molecular structure slides called MolSlides. See examples at MolSlides.ProteinExplorer.Org. MolSlides of any molecular view achieved in PE can be saved with a few clicks of the mouse. Advance to the next MolSlide by pressing the spacebar. PE includes a MolSlide Manager for importing sets of MolSlides, merging, re-organizing, and updating. MolSlides can be presented in Chime or Jmol. For more information, please see MolSlides.ProteinExplorer.Org.

Create presentations in PE! Presentations in Protein Explorer (PIPEs) encourage seamless transitions between the author's views of the molecule, and self-directed exploration using PE's QuickViews toolkit. Each and every view can be further explored on the spot if desired, returning to the author's presentation of views whenever appropriate.

Lesson Plans: For peer-reviewed papers on how to use Protein Explorer in teaching, comments from teachers, databases that display results in PE, and more, see Protein Explorer Lesson Plans and Protein Explorer Literature. Also available within Protein Explorer: ready-made slides Introducing Structural Bioinformatics.

The downside: Because Protein Explorer requires the free MDL Chime plugin, it works only in Windows and best in Firefox. It works perfectly in Windows inside Intel Mac OSX.


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! Chime

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



Amino Acid Quizzer Chime       *Win-IE6-Compatible*

The Amino Acid Quizzer challenges students to identify amino acids based on viewing the 3D structure. Requires instructor input. Downloadable.


Alpha Helix Thermal Motion Chime

Raul E. Cachau has provided this Demonstration of animation from XYZ files: 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.    Downloadable

Summary of Visiting and Downloading Rates for This Site.

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