MIME types for Chemistry
Last modified June 20 1997
This project was developed jointly by Henry Rzepa at Imperial College Chemistry Department and Benjamin Whitaker at the Department of Chemistry, Leeds University, UK.
For more information on MIME (Multipurpose Internet Mail Extensions) file types and our specific proposals for chemistry check out the Chemical MIME Home Page . You may also wish to read Chemical Applications of the World-Wide-Web System and Hyperactive Molecules and the World-Wide-Web Information System. These papers appeared in J. Chem. Soc. Chem. Comm. (1994) 1907-1910 and J. Chem. Soc. Perkin Transactions 2 (1995) 7-11 respectively.
The following pages are a step-by-step guide through a number of applications of Chemical MIME type on the Web. You may, however, wish to jump straight to a page describing the full set of configuration details for W3 browsers.
MIME types for molecular geometries
Before we start you may be asking yourself - Why do I want to bother with all this ? Well you may not, but just to give you a sample of what is possible here is a screen image of Mosaic running just after the user has clicked on one of the images on this page.
By using chemical MIME types it is possible to tell the W3 browser that the file associated with the .gif image embedded in this page is to be treated as the source file for a visulisation application. In this way the 3D coordinate data can be viewed as an active (i.e. a user manipulable) object. This allows one to play with the view point and rotate the molecule in space. The visualiser also lets you change the representation of the molecule. In this case from the space-filled representation of the .gif to a ribbon representation in the viewer.
How is it done ?
A common format for describing the structure of large biological molecule is the protein database or "pdb" file. Large databases, such as the `Molecules-R-Us', National Institutes of Health database, the Brookhaven Protein Data Bank or the UK Chemistry Database Service, can be easily accessed through the Web and its gateways. Another common format is XYZ. It is a simple matter to reconfigure a Web browser to view these files through freely available molecular graphics packages.Unix and Mosaic
To reconfigure Mosaic to view these files through the Minnesota Supercomputer Centre's Xmol package you will need to edit your .mailcap file (if you don't already have one create it in your home directory) and add the lines:
- chemical/x-pdb; xmol -readFormat pdb %s
- chemical/x-xyz; xmol -readFormat xyz %s
This defines the chemical MIME type with a secondary characteristic of /x-pdb, and associates it with the viewer on your own system. The x- indicates that this is an experimental MIME type which hasn't officially become accepted.
If you don't have Xmol but have RasMol the same procedure will work if you add the lines
- chemical/x-pdb; xterm -T "RasMol v.2.5.1." -e rasmol -pdb %s
- chemical/x-xyz; xterm -T "RasMol v.2.5.1." -e rasmol -xyz %s
to your .mailcap file (but you will need RasMol2.5 or higher since earlier versions of RasMol doesn't understand the "xyz" format). Actually I generally use
- chemical/x-pdb; xterm -T "RasMol v.2.5.1." -e rasmol -pdb %s
- chemical/x-xyz; xmol -readFormat xyz %s
so that "pdb" files get viewed with RasMol and "xyz" files with Xmol. The choice of viewer is up to you, and you could use any application that understands these file formats. Xmol and RasMol have the advantage that they can be picked up easily by anonymous ftp (and are free). It is also worth pointing out that a number of other file types are supported through chemical MIME types. To pick up the full list you should consult the full specification.
Macintosh and MS Windows
If you are a Macintosh or PC user you may find the discussion here more interesting.
Examples of "pdb" and "xyz" geometry specifications
Assuming that you have RasMol2.5 or Xmol installed on your system and have just edited your configuration files reload your configuration files from the "Options" drop down menu on your browser, and click on the image below.
(H.Ago,J.Kataoka,H.Tsuge,N.Habuka,E.Inagaki,M.Noma, and M.Miyano, "Three dimensional structure of the alpha pokeweed antiviral protein at 2.3 angstroms resolution", picked at random from the Brookhaven Protein Data Bank). HEALTH WARNING the alpha pokeweed protein contains more than 2000 atoms so you may wish to look at something a little more managable
such as buckminsterfullerene.
Other applications of Chemical MIME's
Potential applications of Chemical MIME types include Web interfaces to molecular dynamics and quantum chemistry packages. A demonstration of how this might be done can be found here. Through image sensitive (IS) maps 2D nmr data (such as NOESY spectra) can be linked to molecular graphics packages. A demonstration of what can be done can be found here.We have also been experimenting with the Web as a conferencing medium. To this end we have developed a suite of applications for Iris Explorer. These tools allow us to animate the molecular models. Further details can be found here.
Test out the Synopsys viewer called Accord Interactive Chemistry Viewer for SMILES and other formats (experimental).
You may also wish to check out other methods of rendering molecules in documents. A few demonstrations using the Java XYZ MoleculeViewer from Sun Microsystems are available here. An alternative is to use Cherwell Scientific's ChemSymphony Java molecule viewer.
We are also experimenting with using a World-Wide Web server for teaching applications. For example, in our Department Dr Stuart Green has made use of Chemical MIME types to develop teaching aids for our course on Computer-Aided Drug Design. For other examples of the use of RasMol in teaching applications check out the work of Eric Martz in Massachusetts.
