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.
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.
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.
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.
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