To align two pdb, prot1 and prot2
It may be necessary to restrict the alignment region to certain chains.
For example, to match chain A to chain B:
will align prot1 and prot2 just on the segment shown (90-100).
To avoid refinement of the alignment add 0,0 at the end:
pair_fit will use all atoms, whereas align will only use atoms that are matched with respect to a dynamic-programming sequence alignment. Disadvantage of pair_fit is that the atoms number must be equal.