I have solved a complex structure of two proteins, and a reviewer has asked to compare the altered interface binding of one particular binding partner (protein2) in this complex to various other similar deposited PDBs through r.m.s.d. calculations and rotation/translation matrices.

After aligning ~4 structures from the PDB (specifically aligning 1 chain to the other binding partner, protein1) to my structure, I want to calculated the rmsd before and after re-aligning the deposited structures (containing protein2) to my complexed protein2.

I have used the superpose utility in phenix to align the C-alphas, however, I am getting very large rmsd values after alignment (~3.3). This is rather strange as the aligned proteins are essentially the exact same, both in sequence and secondary structure.  Using various different programs such as SSM, Coot, and others give me an rmsd value of ~1, which is far more reasonable, but they do not output a "start" rmsd value.

Any suggestions on what the cause of this large rmsd value? Or possibly another program that could provide start and final rmsd values along with rotation/translation matrices for alignment?

Thanks,
Bret