PyMOL provides a command called align to align a specific region of structures. The protein structures do not need to have to identical sequence. It’s more flexible than MOLMOL 2k.2.
The command manual copied from PyMOL is pasted here:
DESCRIPTION "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. USAGE align (source), (target) [,cutoff [,cycles [,gap [,extend [,skip [,object [,matrix [, quiet ]]]]]]]] PYMOL API cmd.align( string source, string target, float cutoff=2.0, int cycles=2, float gap=-10.0, float extend=-0.5, float extend=-0.5,int skip=0, string object=None, string matrix="BLOSUM62",int quiet=1 ) NOTE If object is not None, then align will create an object which indicates which atoms were paired between the two structures EXAMPLES align prot1////CA, prot2, object=alignment SEE ALSO fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit
Another external fitting/alignment command is called cealign, you could find a complete description at here (http://www.pymolwiki.org/index.php/Cealign) .
Here are two snapshots before and after I align 1DYR to other 8 DHFR proteins. This time, all proteins have identical sequence; therefore, I use “align 1DYR, 1DAJ” to align 1DYR onto 1DAJ (all atoms to all atoms). The Tcl/Tk GUI window returned a RMS value and several detailed information.