[Chimera-users] mmaker usage with md-movie perframe

Friends, I have a crystal structure of a protein (370aa). I have a trajectory of a similar protein (not same) with (210aa). I opened the crystal structure and the trajectory via md-movie tool. In the perframe analysis, i gave the following command (#1 my traj, #0 crystal.pdb) *mmaker #1 #0 computeSS false* mmaker uses different number of atom pairs for rmsd calculation. If there are say 150aa that match between my target and crystal, then mmaker should make the rmsd firt for 150 atom pairs in every frame. Why does it use different no. of atom pairs. Do i need to give some extra options ? Thanks, Bala -- C. Balasubramanian