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The excellent SSM alogrithm1 of Eugene Krissinel is available in Coot. The GUI interface is straight-forward and can be found under Calculate -> SSM Superpose. You can specify the specific chains that you wish to match using the "Use Specific Chain" check-button.
There is a scripting level function which gives even finer control:
(superpose-with-atom-selection imol1 imol2
mmdb-atom-selection-string-1 mmdb-atom-selection-string-2
move-copy-flag )
the move-copy-flag should be 1 if you want to apply the transformation to a copy of imol2 (rather than imol2 itself). Otherwise, move-copy-flag should be 0.
mmdb atom selection strings (Coordinate-IDs) are explained in detail in the mmdb manual.
Briefly, the string should be formed in this manner:
/mdl/chn/seq(res).ic/atm[elm]:aloc
e.g. "/1/A/12-130/CA"
<p><a href="http://www.ebi.ac.uk/~keb/cldoc/object/cl_obj_surf.html#CoordinateID">The mmdb manual CoordinateID description</a>.</p>