View source for Structural superposition

# [http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchmaker/matchmaker.html MatchMaker] which is part of [http://www.cgl.ucsf.edu/chimera Chimera]
# [http://xray.bmc.uu.se/alwyn/A-Z_of_O/A-Z_frameset.html O]
# [http://xray.bmc.uu.se/usf/lsqman_man.html lsqman]
# [http://www.ccp4.ac.uk/html/lsqkab.html lsqkab]
# [[coot]]
# [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. 
# [http://webapps.embl-hamburg.de/escet/ Escet] good for finding subtle differences, or the common core
# Using CCP4i: go to the coordinate utility - Superpose molecules - You can either compare things using secondary structure or by specifying residue spans. Underlying programs are PISA (also available at the BI msd server) and LSQKAB 
# CCP4: superpose foo_1st.pdb [-s CID1] foo_2nd.pdb [-s CID2] [ foo_out.pdb ]  Only bear in mind that [http://www.ccp4.ac.uk/html/superpose.html superpose] relies on the presence of secondary structure, so that your selections should always include at least 3 SSEs.
# MUSTANG - http://pxgrid.med.monash.edu.au:8080/mustangserver/
# FATCAT - [http://fatcat.burnham.org/fatcat-cgi/cgi/fatcat.pl?-func=pairwise flexible alignment]
# or just choose one of the 84 or so entries in [http://en.wikipedia.org/wiki/Structural_alignment_software Wikipedia]