{+ file: rmsd.inp +}
{+ directory: general +}
{+ description: Calculate RMS coordinate difference between 2 structures +}
{+ comment: 
            calculates overall RMS coordinate difference 
            between the structures and also lists average difference
            for mainchain, sidechain and all atoms as a function
            of residue number +}
{+ authors: Axel T. Brunger, and Paul D. Adams +}
{+ copyright: Yale University +}

{- Guidelines for using this file:
   - all strings must be quoted by double-quotes
   - logical variables (true/false) are not quoted
   - do not remove any evaluate statements from the file -}

{- begin block parameter definition -} define(

{======================= molecular structure =========================}

{* structure file *}
{===>} structure_infile="amy.mtf";

{* reference coordinate file *}
{===>} comp_coordinate_infile="amy.pdb";

{* coordinate file *}
{===>} main_coordinate_infile="amy_anneal.pdb";

{========================== atom selection ===========================}

{* select atoms to be included in calculation *}
{===>} atom_select=(known and not hydrogen);

{* select main chain atoms *}
{* note: atoms outside this selection will be considered to be
         side chain atoms *}
{===>} atom_main=(name ca or name n or name c or name o or name ot+);

{============================== options ==============================}

{* find best fit between structures prior to calculating RMS deviations *}
{+ choice: true false +}
{===>} coord_fit=false;

{=========================== output files ============================}

{* output listing file *}
{===>} list_outfile="rmsd.list";

{===========================================================================}
{        things below this line do not normally need to be changed          }
{===========================================================================}

 ) {- end block parameter definition -}

 checkversion 1.2

 evaluate ($log_level=quiet)

 structure @&structure_infile end

 coordinates disp=comp @&comp_coordinate_infile

 coordinates @&main_coordinate_infile

 if ( &coord_fit = true ) then
   coord fit sele=&atom_select end
 end if

 coord rms sele=&atom_select end
 evaluate ($overall_rmsd=$result)

 set display=&list_outfile end

 display >>>> RMS coordinate deviation calculated between 2 structures:
 display >>>>   structure file= &STRIP%structure_infile
 display >>>>   main coordinate set= &STRIP%main_coordinate_infile
 display >>>>   reference coordinate set= &STRIP%comp_coordinate_infile
 display
 display >>>> overall RMS deviation= $overall_rmsd[f8.4] Angstroms
 display
 display  segid  resid     RMSD   RMSD-main   RMSD-side
 display

 set display=OUTPUT end

 for $id in id ( byres(&atom_select) and tag ) loop rmsd

   show (segid) (id $id)
   evaluate ($segid=$result)
   show (resid) (id $id)
   evaluate ($resid=$result)
   
   show norm(rmsd) ( &atom_select and segid $segid and resid $resid )
   evaluate ($all=$result)

   show norm(rmsd) ( &atom_select and segid $segid and resid $resid and
                     &atom_main )
   evaluate ($main=$result)

   show norm(rmsd) ( &atom_select and segid $segid and resid $resid and
                     not ( &atom_main ) )
   evaluate ($side=$result)

   set display=&list_outfile end
   display  $segid[a4]    $resid[a4]  $all[f8.4]  $main[f8.4]    $side[f8.4]
   set display=OUTPUT end

 end loop rmsd

 stop