Hi Sasi,
for pair_fit you have to match all atom pairs manually. I guess what
you want is align on the full monomers and then rms_cur (or just
distance measure) on each CA pair.
Have a look at the rmsd_b.py script from
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
It writes per
dear pymol users,
i have a homodimer, with two identical monomers. i would like to know the
rmsd of each residue in the first monomer with respect to each residue in
the second monomer.
i guess pair_fit should give the rmsd.
is there a better command to look at the per residue rmsd.
thank you.
