remarks file geomanal/rmsdplot.inp -- Rms difference per residue
remarks Specific for proteins: backbone and sidechain atoms. 

                                                     {*Read structure file.*}
  {===>} structure @../generate/generate.psf end    
     
                                                        {*Read coordinates.*}
  {===>} coordinates @../xtalrefine/slowcool.pdb   
        
                                                  {*Read comparison coords.*}
  {===>} coordinates disposition=comp @../generate/generate.pdb

  {===>} 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>).*}

  coor fit selection=( store9 ) end {*Fit coordinates using selected atoms.*}

                      {* swap equivalent groups to minimize rms difference *}
  @rotares.inp  
              
  coor rms end                     {*Compute rmsds and store in RMSD array.*}

  {===>} set display=rmsdplot.list end   {*Write the rmsds 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 ( rmsd ) ( byresidue ( id $atom_id ) 
                              and ( name ca or name n or name c ) )
      evaluate ( $back=$result )
      vector show norm ( rmsd ) ( byresidue ( id $atom_id )
                              and not ( name ca or name n or name c ) 
                              and not hydrogen )
      evaluate ( $side=$result )
      evaluate ($number=$number+1)
      display  $number  $back   $side
  end loop out2
  

  set echo=on end
  set message=on end
  stop