parm 6nc6_ready.pdb
parm 6nc7.pdb
parm 6nc9_ready.pdb
parm average.pdb 
trajin 6nc6_ready.pdb parmindex 0
trajin 6nc7.pdb parmindex 1
trajin 6nc9_ready.pdb parmindex 2
reference average.pdb [ref] parmindex 3
readdata evecs.dat name myEvecs
strip !@CA
rms reference ref 
projection modes myEvecs out project_native.dat beg 1 end 3 @CA
run