parm 7aaq_renum.pdb
parm 7aar_renum.pdb
parm average.pdb 
trajin 7aaq_renum.pdb parmindex 0
trajin 7aar_renum.pdb parmindex 1
reference average.pdb [ref] parmindex 2 
readdata evecs.dat name myEvecs
strip !:1-32,62-202,262-353,364-395,403-452@CA
rms reference ref 
projection modes myEvecs out project_native.dat beg 1 end 3 @CA
run