parm 5i6x_ready.pdb
parm 6dzz_ready.pdb
parm average.pdb 
trajin 5i6x_ready.pdb parmindex 0
trajin 6dzz_ready.pdb parmindex 1
reference average.pdb [ref] parmindex 2 
readdata evecs.dat name myEvecs
strip !@CA
rms reference ref 
projection modes myEvecs out project_native.dat beg 1 end 3 @CA
run