Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D is provided for Windows and Macintosh, and can be compiled on Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.
Below is a relatively simple sample of what Cn3D can do. There are many more examples in the Tutorial, along with instructions to help new users get started!