read coor pdb HR5546A_R3_em_bcr3.pdb
all
rmsd coor heavy 15A-32A,34A-37A,42A-47A,53A-57A,60A-73A,75A-79A,85A-91A,100A-106A,108A-116A
ave
resOrd_rmsd_heavy
rmsd coor backbone 15A-32A,34A-37A,42A-47A,53A-57A,60A-73A,75A-79A,85A-91A,100A-106A,108A-116A
ave
resOrd_rmsd_bb
write
best.pdb
coor
all
all
pdb
quit