Given that you don't say what you think it might mean, all I can do is
restate it and hope it makes more sense. ;) To calculate feature 2, the
Euclidean distance between residues in two structures, the structures
must be aligned. So SALIGN does this, but that alignment is only a
temporary one; it is used only to determine the values of feature 2. The
final alignment is done in the regular way, by dynamic programming using
*all* features.