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.

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

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Selected Awards and Mentions

(September 25, 1998) Current Contents' academic websites Top 100 sites American Crystallographic Association Newsletter: Spring, 2003 FIVE STARS - PROJECT MERLOT	Netwatch section of Science 282, #5390 (30 October 1998) (January, 2000) top 100 websites Journal of Chemical Education News from Online Vol. 79, No. 7 July 2002
	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]

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How to view the exhibits at The OMM

Assuming you are using >Netscape 3.0, have downloaded and installed Chime (see Required software), and have restarted Netscape, you should now be able to visualize the following B-DNA molecule:

If you see a strange symbol, , instead of DNA, you do not yet have Chime working appropriately. Perhaps you have installed a version of Chime intended for a different operating system, or you have installed Chime in a different directory than the directory your working version of Netscape is in? Try installing again, carefully following instructions at the MDL Chime site.

If you DO see DNA above, you are ready to visit the exhibits at the OMM, but before you do, here are a few tips to enhance your visit. As you explore a display for the first time, it is recommended that you not manipulate the molecules on your own, but rather follow (i.e. click on), in order, the built-in cue buttons that look like this:  (note the effect on the DNA, above - you can now easily distinguish the base pairs and the ribose-phosphate backbone of the molecule). In a given display, text describing a particular molecular feature will be followed by a cue button that will elicit a relevant change in the rendering of the molecule, similar to what you have just seen. If, at any time, you wish to restore the molecule to its starting state, use the reload button of Netscape to refresh the page.

You can also easily change the orientation or rendering of the molecules on your own. Here is a table of mouse commands with indicated results (may we suggest that you print a copy of this for later reference?):

Desired Result	Windows	Macintosh
Activate Chime's menu	Right button	Click, (don't drag)
Rotate X,Y	Left button, drag	Click, drag quickly
Translate X,Y	Ctrl-Right button, drag	Command* click, drag
Rotate Z	Shift-Right button, drag	Shift-Command* click, drag
Zoom	Shift-Left button, drag	Shift click, drag
Slab Plane	Ctrl-Left button, drag	Ctrl click, drag

*On some Macs, the Option (Alt) key has the same effect as the Command key. For example, if you are using Windows, with a cursor in the molecule frame (try it, above!), clicking the left mouse button and dragging will rotate the molecule around the x and y axes. Clicking the right mouse button will activate a menu that allows the following manipulations: