If you wish WebMol to be your default helper application to view PDB structures, you can follow subsequently listed steps. As there already is a type-definition for pdb-files (chemical/x-rasmol to interplay with the marvellous program RasMol or chemical/x-pdb) you will need to replace this.
If you happen to run Netscape:
This will have the effect that links leading to protein structures ending on the defined suffixes will automatically spawn WebMol with that particular structure loaded. Example: Click on 1ppt.pdb
Invonveniences:
You need to have the Java Run Time System on your machine and setting the classpath
might not be straighforward.