Before you start

There are several options available to you to display PDB files.

You can either install a viewer like RASMOL as an external helper for your browser, or install the plugin CHIME.

RASMOL, and its variants, are available from links on pages by Prof. Eric Martz at UMASS, Amherst.

You will need to configure your browser so that it recognises the mime type chemical/x-pdb (x-mdl-molfile) and set the extension for this as .pdb (.mol) (.xyz) etc.

An alternative is to use ORTEP3 for Windows, this can display a variety of file formats, including PDB files. Prof Martz maintains a list of other visualisation software at UMASS.

The recommended method though, is to use CHIME logo a plug-in for Netscape or Internet Explorer from Molecular Design Limited, Information Systems, Inc. (MDL).

MDL used over 10,000 lines from RASMOL in creating CHIME, which is free for academic and non-commercial use. It again runs on a number of different platforms (although more features are available in the Windows release) and when it is installed, it will set up the necessary information on MIME types.

Version 2.6 SP3 of CHIME was released in September 2001. It includes code from our JCAMP-DX viewer.

For help and tutorials on how to use CHIME see the CHIME site at MDL.

Another source of useful information on CHIME and RASMOL is UMass (Amherst). Prof Eric Martz has an extensive set of notes and tutorials and these pages are an excellent starting point if you are considering developing your own web pages featuring molecular displays.

List of PDB files

I have been experimenting with some variations on the original database arrangement of displaying PDB files. There are now 4 different versions which do slightly different things and these developed as I learnt more and more about CHIME and JavaScripts! Check them out for yourselves to see how the scripts operate, and please note that constructive feedback is always welcome.
 Another display, put together for our first year coordination chemistry course, features a Table showing transition metal complexes with common ligands.
I have combined a part time hobby in photography with a part time interest in the chemistry of local fruits and vegetables and put together some pages which I hope will be of interest. In addition, I am collecting material for pages on flavours and colours. These will include PDB and JCAMP-DX files embeded on web pages and feature CHIME.

To see how CHIME and our JCAMP-DX viewer can be used for displaying spectra and molecular graphics with links between the two, see these examples. Note this requires the Windows of CHIME version 2+ to work.

External Links

To see how this type of display can be used to teach point group symmetry, take a look at the pages at Imperial College, UK.

If you are interested in the structures of proteins, then you should check out the excellent arrangement maintained by the Research Collaboratory for Structural Bioinformatics for viewing files in the Brookhaven Protein Database (PDB) format.

Search the NCI structure database of nearly 250,000 compounds via CACTVS or through ChemWeb.

Other sources of PDB files are Dave Woodcock's collection at Okanagan, Canada, especially of Natural Products and the Klotho project collection at Washington of over 400 compounds.

Cn3D is available from NIH and although it does not read a PDB (it uses ASN.1 which is more compressed than PDB) it will write a PDB as output. You will need to set your MIME type to chemical/ncbi-asn1-binary.

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Copyright © 2003 by Robert John Lancashire, all rights reserved.

Created and maintained by Prof. Robert J. Lancashire,
The Department of Chemistry, University of the West Indies,
Mona Campus, Kingston 7, Jamaica.
Created Sept 1996. Links checked and/or last modified 29th January 2003.
URL http://wwwchem.uwimona.edu.jm/spectra/PDBIndex.html