Structural superposition

1. MatchMaker - http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchmaker/matchmaker.html which is part of Chimera http://www.cgl.ucsf.edu/chimera
2. O
3. lsqman
4. lsqkab
5. coot
6. Theseus - http://www.theseus3d.org/ Theseus is a program that simultaneously superimposes multiple macromolecular structures. Instead of using the conventional least-squares criteria, Theseus finds the optimal solution to the superposition problem using the method of maximum likelihood.
7. Escet - http://webapps.embl-hamburg.de/escet/ good for finding subtle differences, or the common core