Protein Explorer became non-operational about 2008. It is replaced with FirstGlance.Jmol.Org (for guided exploration of any macromolecule), and Proteopedia.Org (for authoring customized molecular scenes that are immediately online to share worldwide).
Protein Explorer provides a user interface to the Chime plugin allowing easy manipulation and viewing of PDB structure files. Includes most RasMol commands and has a command line, but has buttons and menus for many useful commands. Includes a comparator funciton that allows comparisons between two structures, molecules in the structure can be selected in a sequence window and there is a non-covalent bond finder function.