< ware >

 

< methods >

The Online
Macromolecular Museum...

...serving biomolecular visualizations
since 1996

 

< mentions >

 

< exhibits >

 


About this site

museum definition: an institution, building, or room for preserving, studying, and exhibiting artistic, historical, or scientific objects
n. [L. <Gr. mouseion, place for the muses or for study < mousa, Muse] an institution, building, or room for preserving, studying, and exhibiting artistic, historical, or scientific objects (Webster's Second College Edition Dictionary)

The Online Macromolecular Museum (OMM) is a site for the display and study of macromolecules. Macromolecular structures, as discovered by crystallographic or NMR methods, are scientific objects in much the same sense as fossil bones or dried specimens: they can be archived, studied, and displayed in aesthetically pleasing, educational exhibits. Hence, a museum seems an appropriate designation for the collection of displays that we are assembling. The OMM's exhibits are interactive tutorials on individual molecules in which hypertextual explanations of important biochemical features are linked to illustrative renderings of the molecule at hand.

Why devote a site to detailed visualizations of different macromolecules? In learning about the intricacies of life processes at the molecular level, it is important to understand how natural selection has fashioned the structure and chemistry of macromolecular machines to suit them for particular functions. This understanding is greatly facilitated by the visualization of 3-dimensional structure, when known. So, if static views of molecules (even in stereo) are worth a thousand words, then interactive animations of molecules should be worth much more. Indeed, we have found the types of displays represented here invaluable in gaining an appreciation for the details of key biochemical processes.

As Carl Brandon and John Tooze stated in their classic text, Introduction to Protein Structure:

"Molecular biology began some 40 years ago with the realization that structure was crucial for a proper understanding of function. Paradoxically, the dazzling achievements of molecular genetics and biochemistry led to the eclipse of structural studies. We believe the wheel has now come full circle, and those very achievements have increased the need for structural analysis at the same time that they have provided the means for it." 

It is our opinion that structural analysis should extend into the classroom: as students learn about cellular mechanisms it is important that they study the chemistry of the molecular machines involved. These considerations have motivated the construction of the OMM.

The OMM is part of a collaborative effort by faculty and students interested in macromolecular structure-function relationships. The primary authors of some tutorials are students of David Marcey and he serves as author, co-author and site editor, and assumes all responsibility for content. Any criticisms, suggestions, comments, or questions should be sent to him at: marcey@clunet.edu. All tutorials are copyrighted.

The OMM was started in 1996 for a Molecular Biology class at Kenyon College, Gambier, Ohio, where DM was a professor in the Biology Department (1990-1999). The OMM is now developed and housed at CLU, where DM has been a professor since 1999.

The exhibits are under continual construction. We thank you for your patience, and hope you enjoy the current exhibits.

Contributions of detailed macromolecular tutorials from other sources are welcome! If you are interested in providing additions to the OMM collection, please contact the above.

If you would like an image to use as an icon to link to this site, here is a gif (81x92 pixels - 5K).

[Back to top] [About this site] [Required software] [Links of interest] [Methods]
[How to view the exhibits] [Acknowledgements] [The Exhibits] [Feedback]


Required software

Jmol Exhibits:
  • For MacOSX+ users the Safari Browser works well. Recently problems have been reported with the Google Chrome browser on Macs. This should be remedied soon.
  • For PC users, Firefox, Netscape, Chrome, and IE work well. We recommend Firefox or Chrome.

In the exhibits section, Jmol exhibits are indicated in red.

Chime Exhibits:

In order to view the Chime macromolecular exhibits at the OMM you will need two items:

1. A FRAMES-capable browser, e.g. Firefox.

2. Chemscape Chime, a browser plug-in. Contact us for more info.

For Chime users, a PC or MacOS<10 is required. However, the Jmol exhibits are readily viewed by all (see software, above). In the exhibits section, Jmol exhibits are indicated in red. This site is best viewed with a screen resolution of 1024x768 or higher, although 800x600 still looks satisfactory. We suggest a display of at least 256 colors.

[Back to top] [About this site] [Required software] [Links of interest] [Methods]
[How to view the exhibits] [Acknowledgements] [The Exhibits] [Feedback]


Links of interest

In addition to links related to specific macromolecules (found in individual exhibits), here are a few of the numerous WWW sites concerned with macromolecular modeling that we find particularly useful.
The following links open in a new browser window
.

Where to get PDBs:

The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological molecules, serving a global community of researchers, educators, and students. The PDB, formerly run by the Brookhaven National Laboratory, now has its home at the The Research Collaboratory for Structural Bioinformatics (RSCB).

The Protein Data Bank

Proteopedia - a WIKI site for proteins!

PDB at a glance A functional classification of some PDB entries

SCOP (structural classification of proteins) A great site with proteins classified into structural families, with links to PDB entries, etc..

NIH Center for Molecular Modeling This National Institutes of Health site has info on software, etc., plus links to numerous relevant WWW resources. 

Molecules R US This site allows easy access to the PDB. You may download molecules for immediate viewing of static images, or download molecules as *.pdb files to be viewed with client-side viewers, e.g. RasMol and Chime.

 

Jmol/Chime (RasMol) Sites:

Jmol site. This is place to get started with Jmol.

An Introduction to Jmol Scripting
This OMM exhibit provides example Jmol scripts that can be copied and pasted into your own molecular exhibits. Each section starts with a discussion of the uses of various renderings and ends with a table that includes an extensive list of buttons (left column) containing sample scripts (right column).

The RasMol/Chime Homepage at The University of Mass. (Amherst) This site contains a wealth of valuable information on the RasMol and Chime programs used at the OMM as well as a World Index of Biomolecular Chime tutorials on the WWW. Highly recommended!

The RasMol version 2.6-beta-2/Chime 0.99 manual

How to install RasMol Scripts into Chime

The CMU Chime Tutorial (by Gordon Rule) takes you step-by-step through most of the features of the Chime menu selections.

 

 

 

 

[Back to top] [About this site] [Required software] [Links of interest] [Methods]
[How to view the exhibits] [Acknowledgements] [The Exhibits] [Feedback]


Methods used to construct the molecular exhibits

The exhibits were created by using Jmol scripts to illustrate structural/chemical features of macromolecules. Some of the sites found in the Links of interest section have materials describing the construction of Jmol web pages.

The molecules and scripts are read by Jmol. Most molecular files (*.pdb) were downloaded from the Protein Data Bank. In some cases (noted in individual exhibits), the *.pdb files for particular molecules were modified using Hyperchem or DeepView molecular modeling software, or created de novo with Hyperchem. The *.pdb files are gnu-zipped to minimize download time, but some are still quite large (~1Mb+), so please be patient.

[Back to top] [About this site] [Required software] [Links of interest] [Methods]
[How to view the exhibits] [Acknowledgements] [The Exhibits] [Feedback]


Acknowledgements

The authors wish to thank Roger Sayle for the creation of RasMol, MDL Information Systems, Inc., for Chime, and the federally-funded Protein Data Bank. Thanks to Tim Maffett of MDL Information Systems for helpful advice that got us started in 1996 and for providing online info on Chime scripting. Kudos to Eric Martz (U. Mass.) for promoting RasMol and Chime at his great RasMol/Chime site and for maintaining the RasMol listserve. Special thanks to the Jmol development team for creating the open source applet for molecular pedagogy on the WWW. Please see the Jmol site for more information.

For introducing us to Jmol, for getting us started in Jmol exhibit construction, and for providing key javascripts, a hearty thank you to Tim Driscoll (Molvisions)! Angel Herraez showed us how to implement the Jmol applet in framed web pages, using a suggestion of Bob Hanson's (on the Jmol Discussion list). Angel also provided some javascript that we employ in our exhibits. Thanks to both Angel and Bob! Their molecular visualization websites are BioModel and Cool Molecules, respectively.

Most importantly, thanks to the many structural biologists and chemists whose work is the basis of the OMM displays!

The OMM has been supported by a grant from the W.M. Keck Foundation and by an endowed chair fund made possible by The Fletcher Jones Foundation and CLU.

The W.M. Keck Foundation: benefitting humanity through the disciplines of science and engineering, medical research and higher education


[Back to top] [About this site] [Required software] [Links of interest] [Methods]
[How to view the exhibits] [Acknowledgements] [The Exhibits] [Feedback]


Selected Awards and Mentions

This site was a webpick of The Alchemist Webzine: Issue 9/25/98
(September 25, 1998)


Current Web Contents webpick
Current Contents' academic websites

DaVinci Press
Top 100 sites


American Crystallographic Association
American Crystallographic Association
Newsletter: Spring, 2003


FIVE STARS - PROJECT MERLOT

Project Merlot - peer reviewed websites

OMM featured in Netwatch section of Science 282, #5390, 30 October 1998
Netwatch section of Science 282, #5390 (30 October 1998)


webpick of the HMS Beagle, the webzine of BioMedNet.com
(January, 2000)

Genetic Engineering News
top 100 websites

Journal of Chemical Education
Journal of Chemical Education
News from Online
Vol. 79, No. 7 July 2002

AllLearn  Library
 
A Biochemical Society  Education Resource
A Biochemical Society
Education Resource

The above links open a new window.

[Back to top] [About this site] [Required software] [Links of interest] [Methods]
[How to view the exhibits] [Acknowledgements] [The Exhibits] [Feedback]



How to view the exhibits at The OMM

For the Jmol exhibits (recommended), simply click the radio buttons and explore the molecules. Molecules can be rotated by clicking and dragging. Right clicking on the molecule will open up a menu of commands. Visit the Jmol site for instructions on how to use this menu.

[Back to top] [About this site] [Required software] [Links of interest] [Methods]
[How to view the exhibits] [Acknowledgements] [The Exhibits] [Feedback]