REMARKS  XFFTEST.INP
remarks  test the FFT routines of XRAY 

parameter @CNS_TOPPAR:protein.param end

{* read a ca trace *}
struc 
data_cns_mtf

_cns_mtf.title
; FILENAME="/data/rwgk/test/tmp.mtf"
  DATE:18-Nov-98  14:17:52       created by user: rwgk
  VERSION:0.4a
;

loop_
_cns_mtf_atom.id
_cns_mtf_atom.segment_id
_cns_mtf_atom.residue_id
_cns_mtf_atom.residue_name
_cns_mtf_atom.atom_name
_cns_mtf_atom.chemical_type
_cns_mtf_atom.charge
_cns_mtf_atom.atom_mass
1 ' ' '1' 'LYS' 'CA' 'CH1E' 0.250000 13.0190
2 ' ' '2' 'LYS' 'CA' 'CH1E' 0.250000 13.0190
3 ' ' '3' 'LYS' 'CA' 'CH1E' 0.250000 13.0190
-1 ' ' ' ' ' ' ' ' ' ' -1.00000 -1.00000

loop_
_cns_mtf_bond.id[1]
_cns_mtf_bond.id[2]
-1 -1

loop_
_cns_mtf_angle.id[1]
_cns_mtf_angle.id[2]
_cns_mtf_angle.id[3]
-1 -1 -1

loop_
_cns_mtf_dihedral.id[1]
_cns_mtf_dihedral.id[2]
_cns_mtf_dihedral.id[3]
_cns_mtf_dihedral.id[4]
-1 -1 -1 -1

loop_
_cns_mtf_improper.id[1]
_cns_mtf_improper.id[2]
_cns_mtf_improper.id[3]
_cns_mtf_improper.id[4]
-1 -1 -1 -1

loop_
_cns_mtf_explicit_nonbonded_exclusion.inb
-1

loop_
_cns_mtf_explicit_nonbonded_exclusion.iblo
0
0
0
-1

loop_
_cns_mtf_group_linked_list.first_atom_id
0
1
-1

end

coor 
ATOM      1  CA  LYS     1       8.000   8.000   8.000  1.00 15.00          
ATOM      2  CA  LYS     2       1.400   6.200  18.000  1.00 15.00          
ATOM      3  CA  LYS     3       2.400   9.200  16.000  1.00 15.00          
END 

{===================================================================}
{* test with arbitrary unit cell, P1 space group *}
{===================================================================}

xray
   declare name=fobs type=complex domain=reciprocal end
   declare name=fpart domain=reciprocal type=complex end
   declare name=fcalc domain=reciprocal type=complex end
   declare name=fom domain=reciprocal type=real end
   declare name=weight domain=reciprocal type=real end
   declare name=sigma domain=reciprocal type=real end
   declare name=test domain=reciprocal type=integer end

  tselection=( 3 <= d <= 10 )
  binresolution= 3. 10.
  mapresolution 3.
  
  a=16.2 b=16.5 c=8.2 alpha=81.2  beta=94.5 gamma=100.3

  symmetry=(x,y,z)
  SCATter ( chemical C* ) 
       2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600
  method=direct lookup=false
  nreflections=1000
  generate  10. 3.
  mapresolution 3.
  do (fpart=0) ( all ) 
   predict 
      mode=reciprocal 
      to=fcalc 
      selection=( all ) 
      atomselection=( not hydrogen ) 
   end 
  do (fobs=fcalc) ( all ) 
  TOLERANCE=0.0
  wa=200000.
  do (fom=1.) ( all )
end
coor translate vector=( 1.1  0.8 1.4 ) sele=( resid 1 ) end

flags exclu * inclu xref end  
energy end
do ( xcomp = dx ) ( all )
do ( ycomp = dy ) ( all )
do ( zcomp = dz ) ( all )
xray
   method=fft
   fft bscale=20.0  memory=50000 prime=5 avoid=2 end      
end
energy end
show elem ( dx )    ( all )
show elem ( xcomp ) ( all )
show elem ( dy )    ( all )
show elem ( ycomp ) ( all )
show elem ( dz )    ( all )
show elem ( zcomp ) ( all )
xray fft memory=250 end end
energy end
show elem ( dx ) ( all )
show elem ( dy ) ( all )
show elem ( dz ) ( all )
xray 
    fft memory=5000 bscale=0.0 end    
    predict 
      mode=reciprocal 
      to=fcalc 
      selection=( all ) 
      atomselection=( not hydrogen ) 
    end 
    print target
    fft             bscale=10.0 end   
    predict 
      mode=reciprocal 
      to=fcalc 
      selection=( all ) 
      atomselection=( not hydrogen ) 
    end 
    print target
    fft             bscale=20.0 end   
    predict 
      mode=reciprocal 
      to=fcalc 
      selection=( all ) 
      atomselection=( not hydrogen ) 
    end 
    print target
    fft elim=10.0 end  
    predict 
      mode=reciprocal 
      to=fcalc 
      selection=( all ) 
      atomselection=( not hydrogen ) 
    end 
    print target
    fft elim=3.0 end  
    predict 
      mode=reciprocal 
      to=fcalc 
      selection=( all ) 
      atomselection=( not hydrogen ) 
    end 
    print target
    fft elim=10.0 grid=0.25 end 
    predict 
      mode=reciprocal 
      to=fcalc 
      selection=( all ) 
      atomselection=( not hydrogen ) 
    end 
    print target
    fft elim=7.00 grid=0.33333333 end
end


{===================================================================}
{* test with P21 space group *}
{===================================================================}

xray         
  reset
   declare name=fobs type=complex domain=reciprocal end
   declare name=fpart domain=reciprocal type=complex end
   declare name=fcalc domain=reciprocal type=complex end
   declare name=fom domain=reciprocal type=real end
   declare name=weight domain=reciprocal type=real end
   declare name=sigma domain=reciprocal type=real end
   declare name=test domain=reciprocal type=integer end

  a=16.1 b=16.1 c=8.1 alpha=90.  beta=130. gamma=90.0

  symmetry=(x,y,z)
  symmetry=(-x,y+1/2,-z)
  SCATter ( chemical C* ) 
       2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600
  method=direct lookup=false
  generate 10. 3.
  mapresolution 3.
  do (fpart=0) ( all )

  predict 
      mode=reciprocal 
      to=fcalc 
      selection=( all ) 
      atomselection=( not hydrogen ) 
  end 
  do (fobs=fcalc) ( all ) 
  TOLERANCE=0.0
  wa=200000.
  do (fom=1.) ( all )
end
coor translate vector=( 1.1  0.8 1.4 ) sele=( resid 1 ) end

flags exclu * inclu xref end  
energy end
do ( xcomp = dx ) ( all )
do ( ycomp = dy ) ( all )
do ( zcomp = dz ) ( all )
xray
   method=fft
   fft bscale=20.0  memory=50000   prime=5 avoid=2 end      
end                                                
energy end
show elem ( dx )    ( all )
show elem ( xcomp ) ( all )
show elem ( dy )    ( all )
show elem ( ycomp ) ( all )
show elem ( dz )    ( all )
show elem ( zcomp ) ( all )
xray fft memory=250 end end
energy end
show elem ( dx ) ( all )
show elem ( dy ) ( all )
show elem ( dz ) ( all )

{===============================}
{*  test with P31c space group *}
{==============================*}
                 
xray 
  reset 
   declare name=fobs type=complex domain=reciprocal end
   declare name=fpart domain=reciprocal type=complex end
   declare name=fcalc domain=reciprocal type=complex end
   declare name=fom domain=reciprocal type=real end
   declare name=weight domain=reciprocal type=real end
   declare name=sigma domain=reciprocal type=real end
   declare name=test domain=reciprocal type=integer end

  a=16.00 b=16.00 c=8.00 alpha=90.0 beta=90.00 gamma=120.0
  symmetry=(x,y,z)
  symmetry=(-y,x-y,z)
  symmetry=(y-x,-x,z) 
!  symmetry=(y,x,1/2+z) 
!  symmetry=(-x,y-x,1/2+z) 
!  symmetry=(x-y,-y,1/2+z) 
  SCATter ( chemical C* ) 
       2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600
  method=direct lookup=false
  generate 10. 3. 
  mapresolution 3.
  binresolution 10. 3.
  do (fpart=0) ( all )
  do (fobs=0) ( all ) 
  predict 
      mode=reciprocal 
      to=fcalc 
      selection=( all ) 
      atomselection=( not hydrogen ) 
  end 
  write reflection fobs fcalc sele=( all ) end
  
  statistics
    completeness
    selection=( 3 <= d <= 10 ) 
      output=OUTPUT
  end
  
  do (fobs=fcalc) ( all ) 
  TOLERANCE=0.0     
  wa=200000.
  do (fom=1.) ( all )
end
coor translate vector=( 1.1  0.8 1.4 ) sele=( resid 1 ) end

flags exclu * inclu xref end 
energy end
do ( xcomp = dx ) ( all )
do ( ycomp = dy ) ( all )
do ( zcomp = dz ) ( all )

xray
   method=fft
   fft bscale=20.0  memory=50000  prime=5 avoid=2  end      
end
energy end
show elem ( dx )    ( all )
show elem ( xcomp ) ( all )
show elem ( dy )    ( all )
show elem ( ycomp ) ( all )
show elem ( dz )    ( all )
show elem ( zcomp ) ( all )
xray fft memory=2000 end end
energy end
show elem ( dx ) ( all )
show elem ( dy ) ( all )
show elem ( dz ) ( all )
xray fft memory=250 end end
energy end
show elem ( dx ) ( all )
show elem ( dy ) ( all )
show elem ( dz ) ( all )


{* ============================ *}
{* test with P2(1)3 space group *}
{* ============================ *}
xray
  reset 
   declare name=fobs type=complex domain=reciprocal end
   declare name=fpart domain=reciprocal type=complex end
   declare name=fcalc domain=reciprocal type=complex end
   declare name=fom domain=reciprocal type=real end
   declare name=weight domain=reciprocal type=real end
   declare name=sigma domain=reciprocal type=real end
   declare name=test domain=reciprocal type=integer end

  a=16.00 b=16.00 c=16.00 alpha=90.0 beta=90.00 gamma=90.0
  {* space_group=P2(1)3 *}
  symmetry=(x,y,z)
  symmetry=(z,x,y)
  symmetry=(y,z,x)
  symmetry=(1/2+x,1/2-y,-z)
  symmetry=(1/2+z,1/2-x,-y)
  symmetry=(1/2+y,1/2-z,-x)
  symmetry=(-x,1/2+y,1/2-z)
  symmetry=(-z,1/2+x,1/2-y)
  symmetry=(-y,1/2+z,1/2-x)
  symmetry=(1/2-x,-y,1/2+z)
  symmetry=(1/2-z,-x,1/2+y)
  symmetry=(1/2-y,-z,1/2+x)
  SCATter ( chemical C* )                          
       2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600
  method=direct lookup=false
  generate  10. 3.
  mapresolution 3.
  binresolution 10. 3.
  do (fpart=0) ( all )
  do (fobs=0) ( all ) 
  predict 
      mode=reciprocal 
      to=fcalc 
      selection=( all ) 
      atomselection=( not hydrogen ) 
  end 
  write reflection fobs fcalc sele=( all ) end
  statistics
    completeness
    selection=( 3 <= d <= 10 ) 
      output=OUTPUT
  end
  do (fobs=fcalc) ( all ) 
  TOLERANCE=0.0     
  wa=200000.
  do (fom=1.) ( all )
end
coor translate vector=( 1.1  0.8 1.4 ) sele=( resid 1 ) end

flags exclu * inclu xref end 
energy end
do ( xcomp = dx ) ( all )
do ( ycomp = dy ) ( all )
do ( zcomp = dz ) ( all )

xray
   method=fft
   fft bscale=20.0  memory=50000   prime=5 avoid=2 end      
end
energy end
show elem ( dx )    ( all )
show elem ( xcomp ) ( all )
show elem ( dy )    ( all )
show elem ( ycomp ) ( all )
show elem ( dz )    ( all )
show elem ( zcomp ) ( all )

xray fft memory=1000 end end
energy end
show elem ( dx ) ( all )
show elem ( dy ) ( all )
show elem ( dz ) ( all )


{* check sorting of reflections *}

xray 
    method=FFT
    
    evaluate ($lr=7.01)
    evaluate ($hr=4.01) 
    binresolution $lr $hr 
    mapresolution $hr
    tselection=( $hr <= d <= $lr ) 
    
    fft grid=0.15 memory=500000 end 
    do (fom=1) ( all ) 
end
energy end
show elem ( dx ) ( all )
show elem ( dy ) ( all )
show elem ( dz ) ( all )

xray
    method=direct lookup=false
end
energy end
show elem ( dx ) ( all )
show elem ( dy ) ( all )
show elem ( dz ) ( all )

{* check partial turning off phase information *}
xray
    evaluate ($lr=6.01)
    evaluate ($hr=5.01) 
    binresolution $lr $hr 
    mapresolution $hr
    tselection=( $hr <= d <= $lr ) 
    
    do (FOM = 0) ( 5.01 <= d <= 6.01 ) 
    
    evaluate ($lr=7.01)
    evaluate ($hr=4.01) 
    binresolution $lr $hr 
    mapresolution $hr
    tselection=( $hr <= d <= $lr ) 
    
end
energy end
show elem ( dx ) ( all )
show elem ( dy ) ( all )
show elem ( dz ) ( all )

xray
    method=FFT 
end
energy end
show elem ( dx ) ( all )
show elem ( dy ) ( all )
show elem ( dz ) ( all )

stop