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

Bala subramanian bala.biophysics at gmail.com
Thu Nov 27 07:02:34 PST 2014


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 ?


C. Balasubramanian
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