read coor pdb BER31_R3_em_bcr3.pdb
all
rmsd coor heavy 14A-16A,21A-24A,27A-37A,40A-44A,46A-63A,89A-95A,100A-146A
ave
resOrd_rmsd_heavy
rmsd coor backbone 14A-16A,21A-24A,27A-37A,40A-44A,46A-63A,89A-95A,100A-146A
ave
resOrd_rmsd_bb
write
best.pdb
coor
all
all
pdb
quit