{+ file: model_mask.inp +}
{+ directory: general +}
{+ description: Make mask from atomic coordinates of 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;

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

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

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

{* select atoms to be included in mask calculation *}
{* a mask will be made around all selected atoms, including 
   atoms generated by any strict NCS operators defined above *}
{===>} atom_select=(known and not hydrogen);

{========================== mask parameters ==========================}

{* Resolution of mask *}
{===>} high_res=3.0;

{* grid spacing as a fraction of the highest resolution limit *}
{===>} grid=0.33;

{* 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;

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

{* output mask *}
{===>} mask_outfile="model.mask";

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

   mapresolution=&high_res
   fft
     grid=&grid
     if ( &fft_memory < 0 ) then
       automemory=true
     else
       memory=&fft_memory
     end if
   end

 end                  

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

 xray                
   declare name=mask domain=real end
   mask
     average=true
     mode=vdw
     solrad=1.0
     shrink=1.0
     nshell=1
     to=mask
     selection=( &atom_select ) 
   end
   write mask
     from=mask
     output=&mask_outfile
     cushion=10.0
     type=omask
   end
 end
 
 stop