About this site
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:
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: firstname.lastname@example.org. 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).
In the exhibits section, Jmol exhibits are indicated in red.
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.
Links of interest
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.
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.
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.
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.
Selected Awards and Mentions
The above links open a new window.
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.