#CCP4I VERSION CCP4Interface 1.3.8
#CCP4I SCRIPT DEF phaser_EP
#CCP4I DATE 26/11/02
#CCP4I USER ameb

EP_MODE                         _mode_ep                      SAD
EP_SAMR                         _logical                      0
LABIN_F                         _logical                      1

#for script file
INPUT_FILES                     _list_of_text                 ""
OUTPUT_FILES                    _list_of_text                 ""
PDB_FILE                        _text                         ""
MTZ_FILE                        _text                         ""
MTZ_DEBUG_FILE                  _text                         ""
SOL_FILE                        _text                         ""
SUM_FILE                        _text                         ""
PDB_HAND_FILE                   _text                         ""
MTZ_HAND_FILE                   _text                         ""
SOL_HAND_FILE                   _text                         ""

#ATOMS
HA_SITES_OPTION_SAD             _atom_option                  HYSS
N_HA_SAD                        _positiveint                  1
HA_ATOM_TYPE_SAD,0              _text                         ""
HA_ATOM_FRAC_SAD,0              _coord_frac                   FRAC
HA_ATOM_X_SAD,0                 _fraction                     ""
HA_ATOM_Y_SAD,0                 _fraction                     ""
HA_ATOM_Z_SAD,0                 _fraction                     ""
HA_ATOM_O_SAD,0                 _real                         ""
HA_ATOM_B_SAD,0                 _real                         ""
HA_ATOM_TYPE_SAD,1              _text                         ""
HA_ATOM_FRAC_SAD,1              _coord_frac                   FRAC
HA_ATOM_X_SAD,1                 _fraction                     ""
HA_ATOM_Y_SAD,1                 _fraction                     ""
HA_ATOM_Z_SAD,1                 _fraction                     ""
HA_ATOM_O_SAD,1                 _real                         ""
HA_ATOM_B_SAD,1                 _real                         ""
#short atoms
HA_SITES_OPTION_MRSAD           _atom_option_short            PDB
N_HA_MRSAD                      _positiveint                  1
HA_ATOM_TYPE_MRSAD,0            _text                         ""
HA_ATOM_FRAC_MRSAD,0            _coord_frac                   FRAC
HA_ATOM_X_MRSAD,0               _fraction                     ""
HA_ATOM_Y_MRSAD,0               _fraction                     ""
HA_ATOM_Z_MRSAD,0               _fraction                     ""
HA_ATOM_O_MRSAD,0               _real                         ""
HA_ATOM_B_MRSAD,0               _real                         ""
HA_ATOM_TYPE_MRSAD,1            _text                         ""
HA_ATOM_FRAC_MRSAD,1            _coord_frac                   FRAC
HA_ATOM_X_MRSAD,1               _fraction                     ""
HA_ATOM_Y_MRSAD,1               _fraction                     ""
HA_ATOM_Z_MRSAD,1               _fraction                     ""
HA_ATOM_O_MRSAD,1               _real                         ""
HA_ATOM_B_MRSAD,1               _real                         ""
#files
HA_FILE_HA_SAD                  _ha_file                      ""
HA_FILE_PDB_SAD                 _pdb_file                     ""
HA_FILE_SOL_SAD                 _sol_file                     ""
DIR_HA_FILE_HA_SAD              _default_dirs                 ""
DIR_HA_FILE_PDB_SAD             _default_dirs                 ""
DIR_HA_FILE_SOL_SAD             _default_dirs                 ""
#bfactors
TOG_CHANGE_BFAC                 _logical                      0
CHANGE_BFAC_ONOFF               _onoff                        ON
TOG_CHANGE_SCAT                 _logical                      0
CHANGE_SCAT_ONOFF               _onoff                        OFF
ATOM_SCAT                       _text                         ""
TOG_ADDITIONAL_ATOMS            _logical                      0
TOG_ADDITIONAL_ATOMS_BAK        _logical                      0
SHOW_HYSS                       _logical                      1
SHOW_SHELX                      _logical                      1

#BINS
TOG_BINS                        _logical                      0
BINS_MIN                        _positiveint                  6
BINS_MAX                        _positiveint                  50
BINS_WIDTH                      _positiveint                  500

#BFACTOR
TOG_WILSON                      _logical                      0
WILSON_ONOFF                    _onoff                        ON
WILSON_SIGMA                    _positivereal                 5
TOG_SPHERICITY                  _logical                      0
SPHERICITY_ONOFF                _onoff                        ON
SPHERICITY_SIGMA                _positivereal                 5

#CELL
TOG_CELL                        _logical                      0
CELL_1                          _positivereal                 ""
CELL_2                          _positivereal                 ""
CELL_3                          _positivereal                 ""
CELL_4                          _positivereal                 ""
CELL_5                          _positivereal                 ""
CELL_6                          _positivereal                 ""

#CLUSTER
TOG_CLUSTER                     _logical                      0
CLUSTER_ID                      _text                         ""
CLUSTER_FILE_PDB                _pdb_file                     ""
DIR_CLUSTER_FILE_PDB            _default_dirs                 ""
TOG_CLUSTER_MR                  _logical                      0
CLUSTER_ID_MR                   _text                         ""
CLUSTER_FILE_PDB_MR             _pdb_file                     ""
DIR_CLUSTER_FILE_PDB_MR         _default_dirs                 ""

#COMPOSITION
SCATTERING                      _composition_option           COMPONENT
#component
N_COMPONENT                     _positiveint                  1
PROTDNA,0                       _protnucleic                  PROTEIN
COMP_OPTION,0                   _mwseqnres_option             FASTA
COMP_OPTION,1                   _mwseqnres_option             FASTA
MW,0                            _positiveint                  ""
MW,1                            _positiveint                  ""
ASYM,0                          _positiveint                  1
ASYM,1                          _positiveint                  1
COMP_FILE,0                     _seq_file                     ""
COMP_FILE,1                     _seq_file                     ""
DIR_COMP_FILE,0                 _default_dirs                 ""
DIR_COMP_FILE,1                 _default_dirs                 ""
COMP_NRES,0                     _positiveint                  ""
COMP_NRES,1                     _positiveint                  ""
#solvent
SCATTERING_SOLVENT              _positivereal                 0.55

#CRYSTAL
HARVEST_PNAME                   _text                         ""
HARVEST_DNAME                   _text                         ""
Fp_SAD                          _mtz_label_g                  ""
SIGFp_SAD                       _mtz_label_sig                ""
Fn_SAD                          _mtz_label_g                  ""
SIGFn_SAD                       _mtz_label_sig                ""
#DEBUG
TOG_VERBOSE_EXTRA               _logical                      0

#HAND
TOG_HAND_OPTION                 _logical                      0 
HAND_ONOFF                      _hand_option                  BOTH

#HKLIN
HKLIN                           _MTZ_file                     ""
DIR_HKLIN                       _default_dirs                 ""

#HKLOUT
TOG_HKLOUT                      _logical                      0
HKLOUT_ONOFF                    _onoff                        ON

#KEYWORDS
TOG_SCRIPT                      _logical                      0
SCRIPT_ONOFF                    _onoff                        ON

#LLGC
TOG_LLGC_SAD                    _logical                      0
LLGC_COMPLETE_SAD               _llgc_complete                DEFAULT
TOG_LLGC_SAD_SIGMA              _logical                      0
LLGC_SIGMA_SAD                  _positivereal                 6.0
TOG_LLGC_SAD_CLASH              _logical                      0
LLGC_CLASH_DEFAULT              _onoff                        ON
LLGC_CLASH_DISTANCE             _positivereal                 2.0
TOG_LLGC_SAD_NCYC               _logical                      0
LLGC_NCYC                       _positiveint                  50
#====
LLGC_FIRST_TYPE                 _text                         ""
N_LLGC                          _positiveint                  0
LLGC_TYPE,0                     _text                         ""
TOG_LLGC_SAD_ATOM               _logical                      0
TOG_LLGC_SAD_REAL               _logical                      0
TOG_LLGC_SAD_ANOM               _logical                      0
#=====
TOG_LLGC_SAD_MAPS               _logical                      0
LLGC_MAPS                       _onoff                        OFF
TOG_LLGC_SAD_METH               _logical                      0
LLGC_METHOD                     _llgc_method                  ATOMTYPE

#MACA
TOG_ANISO                       _logical                      0
MACA_PROTOCOL                   _protocol                     DEFAULT
N_MACA                          _positiveint                  1
MACA_ANIS,0                     _onoff                        ON
MACA_BINS,0                     _onoff                        ON
MACA_SOLK,0                     _onoff                        OFF
MACA_SOLB,0                     _onoff                        OFF
MACA_NCYC,0                     _positiveint                  50

#MACSAD
MACSAD_OPTION                   _protocol                     DEFAULT
TOG_MACSAD                      _logical                      0
TOG_MACSAD_PART                 _logical                      0
N_MACSAD                        _positiveint                  1
TOG_MACSAD_K,0                  _logical                      0 
TOG_MACSAD_B,0                  _logical                      0 
TOG_MACSAD_SIGMA,0              _logical                      0 
TOG_MACSAD_XYZ,0                _logical                      0 
TOG_MACSAD_OCC,0                _logical                      0 
TOG_MACSAD_BFAC,0               _logical                      0 
TOG_MACSAD_FDP,0                _logical                      0 
TOG_MACSAD_SA,0                 _logical                      0 
TOG_MACSAD_SB,0                 _logical                      0 
TOG_MACSAD_SP,0                 _logical                      0 
TOG_MACSAD_SD,0                 _logical                      0 
TOG_MACSAD_PK,0                 _logical                      0 
TOG_MACSAD_PB,0                 _logical                      0 
MACSAD_NCYCL,0                  _positiveint                  ""
TOG_MACSAD_K,1                  _logical                      0 
TOG_MACSAD_B,1                  _logical                      0 
TOG_MACSAD_SIGMA,1              _logical                      0 
TOG_MACSAD_XYZ,1                _logical                      0 
TOG_MACSAD_OCC,1                _logical                      0 
TOG_MACSAD_BFAC,1               _logical                      0 
TOG_MACSAD_FDP,1                _logical                      0 
TOG_MACSAD_SA,1                 _logical                      0 
TOG_MACSAD_SB,1                 _logical                      0 
TOG_MACSAD_SP,1                 _logical                      0 
TOG_MACSAD_SD,1                 _logical                      0 
TOG_MACSAD_PK,1                 _logical                      0 
TOG_MACSAD_PB,1                 _logical                      0 
MACSAD_NCYCL,1                  _positiveint                  ""

#OUTLIER
TOG_OUTLIER                     _logical                      0
OUTLIER_OPTION                  _onoff                        ON
OUTLIER_PROB                    _fraction                     0.000001

#PARTIAL
PART_PDB_MTZ                    _pdb_mtz_option               PDB
PARTPDB                         _pdb_file                     ""
DIR_PARTPDB                     _default_dirs                 ""
PARTMTZ                         _MTZ_file                     ""
DIR_PARTMTZ                     _default_dirs                 ""
PARTIAL_RMSID                   _positivereal                 ""
PARTIAL_RMSID_OPTION            _rmsid_option                 IDENT

#RESOLUTION
TOG_RESOLUTION                  _logical                      0
RESOLUTION_DMAX                 _positivereal                 ""
RESOLUTION_DMIN                 _positivereal                 ""

#ROOT
ROOT                            _text                         ""
FILENAME_ROOT                   _text                         ""

#SCATTERING
TOG_SCAT_MEASURED               _logical                      0
SCAT_TYPE                       _text                         ""
SCAT_FP                         _real                         ""
SCAT_FDP                        _real                         ""
SCAT_REF                        _scat_edge                    EDGE
TOG_SCAT_RESTRAIN               _logical                      0
SCAT_RESTRAIN                   _onoff                        ON
SCAT_SIGMA                      _real                         0.2

#SPACEGROUP
FILE_SPACEGROUP                 _space_group                  ""
EDIT_SPACEGROUP                 _text                         ""

#TITLE
TITLE                           _title_text                   ""

#TNCS
TOG_TNCS_USE                    _logical                       0
TNCS_USE                        _onoff                         ON
TOG_TNCS_ROT_ANGLE              _logical                       0
TNCS_ROT_ANGLE_X                _real                          0                 
TNCS_ROT_ANGLE_Y                _real                          0                 
TNCS_ROT_ANGLE_Z                _real                          0                 
TOG_TNCS_ROT_RANGE              _logical                       0                 
TNCS_ROT_RANGE                  _real                          ""                 
TOG_TNCS_ROT_SAMPLING           _logical                       0                 
TNCS_ROT_SAMPLING               _real                          ""                 
TOG_TNCS_TRA_VECTOR             _logical                       0                 
TNCS_TRA_VECTOR_X               _real                          ""                 
TNCS_TRA_VECTOR_Y               _real                          ""                 
TNCS_TRA_VECTOR_Z               _real                          ""                 
TOG_TNCS_VAR_RMSD               _logical                       0             
TNCS_VAR_RMSD                   _real                          0.4                
TOG_TNCS_VAR_FRAC               _logical                       0                 
TNCS_VAR_FRAC                   _real                          1.0                
TOG_TNCS_PATT_RESO              _logical                       0                 
TNCS_PATT_HIRES                 _real                          5                  
TNCS_PATT_LORES                 _real                          10                 
TOG_TNCS_PATT_PERCENT           _logical                       0                 
TNCS_PATT_PERCENT               _real                          20                
TOG_TNCS_PATT_DISTANCE          _logical                       0                 
TNCS_PATT_DISTANCE              _real                          15                 
TOG_TNCS_LINK                   _logical                       0                 
TNCS_LINK_RESTRAINT             _onoff                         ON                
TNCS_LINK_SIGMA                 _real                          0.1     
TOG_TNCS_PAIR_ONLY              _logical                       0                 
TNCS_PAIR_ONLY                  _onoff                         ON             

#VERBOSE
TOG_VERBOSE                     _logical                      0

#WAVELENGTH
WAVELENGTH                      _positivereal                 ""

#XYZOUT
TOG_XYZOUT                      _logical                      0
XYZOUT_ONOFF                    _onoff                        ON

@ [FileJoin [GetEnvPath CCP4I_TOP] tasks harvest.def]
  

#SHELX and hyss 
TOG_ATOMSEARCH     _logical                1
ATOMSEARCH         _atom_search_option     SHELXD
RUNHYSS            _logical                0
RUNSHELXD          _logical                0
HYSS_INSTALLED     _logical                1
SHELXD_INSTALLED   _logical                1
ATOMSEARCH_INSTALLED   _logical            1
ATOMSEARCH_BOTH_INSTALLED   _logical       1
N_HYSS             _positiveint            ""
HYSS_TYPE          _text                   ""
TOG_HYSS_SEARCH    _logical                0
HYSS_SEARCH        _hyss_search            FAST
HYSS_PDB_FILE      _text                   ""
TOG_HYSS_PHASER    _logical                0
SHELXD_PDB_FILE    _text                   ""
TOG_SHELXC_RESO    _logical                0
MAX_RESO           _resolution             ""
MIN_RESO           _resolution             ""
TOG_NTRY           _logical                ""
NTRY               _positiveint            100
MIND               _positivereal           3.5
ALLOW_SPECIAL_POS  _logical                0
TOG_HYSS_SOLVENT   _logical                0
TOG_MIND           _logical                0

#Parrot and Buccaneer
RUNPARROT          _logical                1
FPwrk              _mtz_label_fo           ""
SIGFPwrk           _mtz_label_sig          ""
FREER              _mtz_label_freer        ""
PARROT_PDB_FILE    _text                   ""
HKLIN_PARROT       _MTZ_file               ""
DIR_HKLIN_PARROT   _default_dirs           ""

RUNBUCCANEER       _logical                1
