Hi  All Pymol users

I have a set of 40 X-ray crystallographic structures complexed with inhibitors belonging to a specific family of kinases. Binding site residues within 5 angstrom from the inhibitor were selected for each PDB structure and saved separately. Now i have a set of 40 PDB files which has only the binding site residues.

I want to perform RMSD for ALL ATOMS against ALL ATOMS. The first structure should be fixed and compared with the remaining 39 structures. For the next time, second structure is fixed and so on for all the 40 structures. Literally it should look like a 40X40 matrix table.

I used align, fit and rms commands. Each one gives different values. Which is the best? Can you help me?

Thank you in advance