theseus 1.4.3-2 (powerpc binary) in ubuntu lucid

 Theseus is a program that simultaneously superimposes multiple
 macromolecular structures. Theseus finds the optimal solution to the
 superposition problem using the method of maximum likelihood. By
 down-weighting variable regions of the superposition and by correcting for
 correlations among atoms, the ML superposition method produces very
 accurate structural alignments.
 .
 When macromolecules with different residue sequences are superimposed,
 other programs and algorithms discard residues that are aligned with
 gaps. Theseus, however, uses a novel superimposition algorithm that
 includes all of the data.