About this site

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.

Fortunately, structural biology has experienced a renaissance in the past decade, yielding structures for many important macromolecules, and the explosion of structural determination continues. As Carl Brandon and John Tooze stated in their 1991 text, Introduction to Protein Structure:

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 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 at Kenyon College, where DM was a professor in the Biology Department (1990-1999). The OMM is now being developed here at CLU., partly in conjunction with a Macromolecular Structure class.

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).

You will need to fill in a short registration form for MDLI. Then follow the links to download Chemscape Chime for whatever operating system you are running. Then install Chime as follows:

Download Chime to a temporary directory (folder)

Run the self-extracting program. Follow the directions of the installer. Be sure that the installer chooses to install into the directory containing your default version of Netscape.

If using Netscape 7.x or Firefox, move the chime.dll file into your plugins directory. 

If you have obtained Chime and it is working appropriately, the B-DNA molecule in the How to view the exhibits section should be visible.

Hardware

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

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.

The exhibits were created by using RasMol/Chime 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 Chime web pages. In addition, instructions on how to build OMM-like tutorials are provided here:

1) How to make an OMM-like molecular exhibit
2) An Introduction to Chime Scripting (requires prior installation of Chime)

The molecules and scripts are read by Chemscape Chime (see Required software). 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 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.