Cn3D is a helper application that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.
Swiss Pdb Viewer
Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank.