Package: Rasmol
In Debian: yes
Web: http://www.umass.edu/microbio/rasmol/index2.htm
Description
Rasmol is a very well known software for viewing molecules in 3D. It supports .pdb file format, and large set of such files are available on the internet.
French presentation: http://logiciels-libres-cndp.ac-versailles.fr/pedagogie/rasmol.html