Sequential internal distance initial point

This option will start the alignment from an alignment performed from pseudo-structures built from the internal distances of the two structures provided [ref]. Since the internal distance matrix provides the whole structural information, this approximation is, many times, enough to provide an initial point very close to the optimal alignment, particularly for sequential bijective structures, as proteins. For non-sequential alignments, this approximation may not be useful, but you will not loose anything by leaving it checked, unless your structures are very, very large (tenths of thousands of atoms), in which case the the program will take a little bit longer to finish.