  The usual Euclidean distance may be generalized to extended objects such as
polymers or membranes. Here, this distance is used for the first time as a cost
function to align structures. We examined the alignment of extended strands to
idealized beta-hairpins of various sizes using several cost functions,
including RMSD, MRSD, and the minimal distance. We find that using minimal
distance as a cost function typically results in an aligned structure that is
globally different than that given by an RMSD-based alignment
