Now, I want to do do a mutliple alignment of many structures (~100) off a single reference structure, and output a text record of the residue pairings involved in the individual alignments along with their RMSD.  

In this particular case, I'll be looking at only small sequence variations of the same protein (with different drugs and cofactors). Accordingly,  I would also like to output the RMSD of residue pairs beyond the alignment cut for relatively easy  identification of regions having maximal variations. 

Advise is appreciated,

With regard,

Jim