remarks file nnr/average_plot.inp -- Rmsds per residue
remarks Specific for proteins: backbone and side-chain atoms. 

{====>}                                              {*Read structure file.*}
structure @g_protein.psf end         

{====>} 
coordinates @average.pdb                                {*Read coordinates.*}

{====>} 
vector ident (store9) ( tag )             {*This selects all residues to be*}
                                          {*analyzed.  Change it           *}
                                          {to analyze portions,            *}
                                          {*e.g., ( tag and segid "A" );   *}
                                          {*"tag" assigns one unique atom * }
                                          {*per residue  (see <selection>).*}
                 

{====>} 
set display=average_plot.list end 
                                        {*Write the plot information to the*}
                                        {*specified file.                  *} 

set echo=off end                          {*Turn off echo to reduce output.*}
set message=off end                            {*Turn off warning messages.*}

evaluate ($number=0)
for $atom_id in id ( store9 ) loop out2
   vector show norm ( b ) ( byresidue ( id $atom_id ) 
                            and ( name ca or name n or name c ) )
   evaluate ( $back=$result )
   vector show norm ( b ) ( byresidue ( id $atom_id )
                            and not ( name ca or name n or name c ) 
                            and not hydrogen )
   evaluate ( $side=$result )
   vector show elem ( resid ) ( id $atom_id )

   evaluate ($number=$number+1)
   display   $number $back $side 
end loop out2

set echo=on end
set message=on end

stop