{+ file: model_fcalc.inp +}
{+ directory: xtal_util +}
{+ description: Generate Fcalc from a model +}
{+ 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) must not be quoted
   - do not remove any evaluate statements from the file -}

{- begin block parameter definition -} define(

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

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

{* parameter files *}
{===>} parameter_infile_1="CNS_TOPPAR:protein_rep.param";
{===>} parameter_infile_2="";
{===>} parameter_infile_3="";
{===>} parameter_infile_4="";
{===>} parameter_infile_5="";

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

{====================== crystallographic data ========================}

{* space group *}
{* use International Table conventions with subscripts substituted
   by parenthesis *}
{===>} sg="P2(1)2(1)2(1)";

{* unit cell parameters in Angstroms and degrees *}
{+ table: rows=1 "cell" cols=6 "a" "b" "c" "alpha" "beta" "gamma" +}
{===>} a=61.76;
{===>} b=40.73;
{===>} c=26.74;
{===>} alpha=90;
{===>} beta=90;
{===>} gamma=90;

{* anomalous f' f'' library file *}
{* If a file is not specified, no anomalous contribution will be included *}
{+ choice: "CNS_XRAYLIB:anom_cu.lib" "CNS_XRAYLIB:anom_mo.lib" "" user_file +}
{===>} anom_library="";

{* resolution limits *}
{+ table: rows=1 "resolution" cols=2 "lowest" "highest" +}
{===>} low_res=500.0;
{===>} high_res=2.0;

{* memory allocation for FFT calculation *}
{* this will be determined automatically if a negative value is given
   otherwise the specified number of words will be allocated *}
{===>} fft_memory=-1;

{=================== non-crystallographic symmetry ===================}

{* NCS-constraints file *}
{* see auxiliary/ncs.def *}
{===>} ncs_file="";

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

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

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

{* output: complex reciprocal space array with model amplitudes and phases *}
{*         do not use the reserved name "fcalc" here *}
{===>} out_f="fc_1";

{* output reflection file *}
{===>} reflection_outfile="model_fcalc.hkl";

{===========================================================================}
{         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 @&coordinate_infile

 parameter
   if ( &BLANK%parameter_infile_1 = false ) then
      @@&parameter_infile_1
   end if
   if ( &BLANK%parameter_infile_2 = false ) then
      @@&parameter_infile_2
   end if
   if ( &BLANK%parameter_infile_3 = false ) then
      @@&parameter_infile_3
   end if
   if ( &BLANK%parameter_infile_4 = false ) then
      @@&parameter_infile_4
   end if
   if ( &BLANK%parameter_infile_5 = false ) then
      @@&parameter_infile_5
   end if
 end

 xray

   @CNS_XTALLIB:spacegroup.lib (sg=&sg;)

   a=&a b=&b c=&c  alpha=&alpha beta=&beta gamma=&gamma

   @CNS_XRAYLIB:scatter.lib

   binresolution &low_res &high_res
   mapresolution &high_res

   generate &low_res &high_res

 end

 if ( &BLANK%anom_library = false ) then
   @@&anom_library
   xray anomalous=true end
 end if

 {- BEGIN MODIFICATION -}
 set echo=off end
 evaluate ($array_name=&STRIP%out_f)
 if ($array_name = "FCALC") then
    display 
    display  error: do not use reserved name "fcalc" for output array
    display  aborting script
    display 
    abort
 end if
 {- END MODIFICATION -}
 
 xray

   query name=&STRIP%out_f domain=reciprocal end
   if ( $object_exist = false ) then
      declare name=&STRIP%out_f domain=reciprocal type=complex end
   end if
   associate &STRIP%out_f ( &atom_select )

   tselection=( all )

   cvselection=( none )

   method=FFT          
   
   fft
     if ( &fft_memory < 0 ) then
       automemory=true
     else
       memory=&fft_memory
     end if
   end

   tolerance=0.0 lookup=false

 end                  

 if ( &BLANK%ncs_file = false ) then
    inline @&ncs_file
 end if

 xray
    predict
      mode=reciprocal
      to=&STRIP%out_f
      selection=( all )
      atomselection=( &atom_select ) 
    end
 end

 xray
   write reflection
     output=&reflection_outfile
     sele=(all)
   end
 end
 
 stop