Structural superposition
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- MatchMaker - http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchmaker/matchmaker.html which is part of Chimera http://www.cgl.ucsf.edu/chimera
- O
- lsqman
- lsqkab
- coot
- 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.
- Escet - http://webapps.embl-hamburg.de/escet/ good for finding subtle differences, or the common core