parm 6xpf_ready.pdb
parm 6xpd_ready.pdb
parm averageMD.pdb 
trajin 6xpf_ready.pdb parmindex 0
trajin 6xpd_ready.pdb parmindex 1
reference averageMD.pdb [ref] parmindex 2 
readdata evecsMD.dat name myEvecs
strip !:1-58,73-128,134-194@CA
rms reference ref 
projection modes myEvecs out project_nativeMD.dat beg 1 end 3 @CA
run