Chemscape Chime by MDL Information Systems is a free plug-in program for Netscape Navigator (version 2.0 and higher) or Microsoft Internet Explorer (3.0 and higher). Chime enables the browser to view a type of file called a "pdb", or Protein Data Bank, file.
Protein Data Bank files were developed to aid in the visualization of three-dimensional protein structures. These 3-d models provide information on molecules ranging from the overall shape of the molecule to its atomic composition. PDB files can be obtained from many sources on the Internet. Some of the more notable sources of these files may be Molecules R'Us from the National Institute of Health and Klotho: Biochemical Compounds Declarative Database. A Swiss-Prot entry will provide a direct link to a PDB file if one exists for the protein it is describing.
The plug-in is available for both the Windows and Macintosh platforms as well as for a number of Unix platforms. Installation instructions should be downloaded as "Read Me" files. Once downloaded, the program files will have to be placed in the Netscape Navigator "plug-ins" folder in order for the plug-in to be recognized by Netscape. Netscape will have to be re-started after installation of the software is complete.
Once the software is installed, Netscape may have to be configured so that it will load the Chime plug-in when it encounters (tries to download) a .pdb file. This may be done as follows:
If you have Chemscape correctly installed on your machine, you should see a model of a short piece of DNA in the table below:
Click on the molecule, hold down the mouse button, and move the mouse. You should be able to rotate the model and view it from from any angle. If you click and holdon the image without moving the mouse, a pop-up menu will appear that gives you many options for changing the appearance of the image and providing additional information. Play with the different features and see what they can do.
Klotho: Biochemical Compounds Declarative Database
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