parm AFmodel_renum.pdb
parm average.pdb 
trajin AFmodel_renum.pdb parmindex 0
reference average.pdb [ref] parmindex 1 
readdata evecs.dat name myEvecs
strip !:9-38,46-70,78-107,123-141,176-210,218-240,246-284@CA
rms reference ref 
projection modes myEvecs out project_native.dat beg 1 end 3 @CA
run