{+ file: rms_fit.inp +}
{+ directory: general +}
{+ description: Calculate and apply RMS coordinate fit between 2 structures +}
{+ comment: 
            calculates the RMS fit between two structures and
            writes out the transformed molecule +}
{+ authors: 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 RMS fit calculation *}
{* the fit will be applied to all the atoms *}
{===>} atom_select=(known and name CA);

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

{* output coordinate file *}
{===>} coordinate_outfile="rms_fit.pdb";

{* format output coordinates for use in o *}
{* if false then the default CNS output coordinate format will be used *}
{+ choice: true false +}
{===>} pdb_o_format=true;

{===========================================================================}
{        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

 coord fit sele=&atom_select end

 if ( &pdb_o_format = true ) then
   write coordinates format=PDBO output=&coordinate_outfile end
 else
   write coordinates output=&coordinate_outfile end
 end if

 stop