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 traditional pictures 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 wonderful 1991 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. Although the primary authors of most tutorials are students of David Marcey, 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: David Marcey: marcey@clunet.edu. All tutorials are copyrighted.

The OMM is under continual construction: the halls are incomplete and some are not yet open. We thank you for your patience!

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 the OMM, here is a gif (81x92 pixels - 5K).

Required software

1. A FRAMES-capable browser. We strongly recommend Netscape Navigator 3.0+ (see browser information), available from Netscape:  

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2. MDL Chemscape Chime(v.2.0 recommended), a wonderful browser plug-in available from MDL Information Systems:

   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. 

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     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.

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 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 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 RCSB is a non-profit consortium dedicated to improving the understanding of the function of biological systems through a study of 3-D biological macromolecular structure. RCSB integrates a variety of production-level data and software resources and shares research results and software. Beyond the PDB, the RCSB develops and maintains a variety of resources of potential interest to the structural biology community. 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, ect.. 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.  The RasMol Version 2.6-beta-2/Chime 0.99 Manual This manual contains the new commands in Chime 0.99 and later, and is a useful reference for RasMol and Chime scripting. See the RasMol Version 2.6-beta-2 Manual for the latest version of the RasMol only manual. Scripting in Chime Chime specific commands used in manipulating molecules. Chime/RasMol Scripting Tutorial Interactive scripting tutorial at MDLI. NIH Center for Molecular Modeling This National Institutes of Health site has info on software, ect., plus links to numerous relevant WWW resources.

Methods used to construct the molecular exhibits

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, we provide instructons on how to build OMM-like tutorials: see How Do I Do This?. The molecules and scripts are read by Chemscape Chime (see Required software). Most molecular files (*.pdb) were downloaded from the Brookhaven 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.

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 (PDB). Special thanks to Tim Maffett of MDL Information Systems for helpful advice that got us started 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! Most importantly, thanks to the many structural biologists and chemists whose work forms the basis of the OMM displays!

Awards and Mentions