align performs a sequence alignment followed by a structural alignment, and then carrys out zero or more cycles of refinement in order to reject structural outliers found during the fit.
align (source), (target) [,cutoff [,cycles [,gap [,extend \ [,skip [,object [,matrix [, quiet ]]]]]]]]
cmd.align( string source, string target, float cutoff=2.0, int cycles=2, float gap=-10.0, float extend=-0.5, int skip=0, string object=None, string matrix="BLOSUM62", int quiet=1 )
If object is not None, then align will create an object which indicates which atoms were paired between the two structures
align prot1////CA, prot2, object=alignment