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

#lists for ccp4 input and output files, in scripts/phaser_ATOM.script
INPUT_FILES                     _list_of_text                  ""
OUTPUT_FILES                    _list_of_text                  ""
PDB_FILE,0                      _text                          ""
MTZ_FILE,0                      _text                          ""
ANO_FILE                        _text                          ""
SUM_FILE                        _text                          ""
SOL_FILE                        _text                          ""
RLIST_FILE                      _text                          ""

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

#COMPOSITION
SCATTERING                      _composition_option            COMPONENT
#component
N_COMPONENT                     _positiveint                   1
PROTDNA,0                       _protnucleic                   PROTEIN
PROTDNA,1                       _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                  ""

#DEBUG
TOG_VERBOSE_EXTRA               _logical                       0

#ENSE
SEARCH_ATOM_TYPE                _text                          ""
SEARCH_ATOM_NUM                 _positiveint                   ""

#ELLG
TOG_USE_ELLG                    _logical                       0                 
USE_ELLG                        _onoff                         ON                 
ELLG_TARGET                     _real                          225             

#HKLIN
HKLIN_MAIN                      _MTZ_file                      ""
DIR_HKLIN_MAIN                  _default_dirs                  ""
TOG_INTENSITY_OPTION            _logical                       1
F                               _mtz_label_f                   ""
SIGF                            _mtz_label_sig                 ""
I                               _mtz_label_j                   ""
SIGI                            _mtz_label_sig                 ""

#HKLOUT
TOG_HKLOUT                      _logical                       0
HKLOUT_ONOFF                    _onoff                         ON

#JOBS
TOG_NJOBS                       _logical                       0
NJOBS                           _positiveint                   4 

#KEYWORDS
TOG_KEYWDS                      _logical                       0
KEYWDS_ONOFF                    _onoff                         ON

#LLGC
TOG_LLGC                        _logical                      1
LLGC_COMPLETE                   _llgc_complete                ON
TOG_LLGC_SIGMA                  _logical                      0
LLGC_SIGMA                      _positivereal                 6.0
TOG_LLGC_CLASH                  _logical                      0
LLGC_CLASH_DEFAULT              _onoff                        ON
LLGC_CLASH_DISTANCE             _positivereal                 2.0
TOG_LLGC_NCYC                   _logical                      0
LLGC_NCYC                       _positiveint                  50
#====
LLGC_FIRST_TYPE                 _text                         "N"
N_LLGC                          _positiveint                  0
LLGC_TYPE,0                     _text                         ""
#=====
TOG_LLGC_MAPS                   _logical                      0
LLGC_MAPS                       _onoff                        OFF

#LABIN
LABIN_MAIN                      _text                          "F SIGF"

#MACA
TOG_ANISO                       _logical                       0
MACA_PROTOCOL                   _macro_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 

#MACM
TOG_MACM                        _logical                       0
MACM_PROTOCOL                   _macro_protocol                DEFAULT
N_MACM                          _positiveint                   1
MACM_ROT,0                      _onoff                         ON
MACM_TRA,0                      _onoff                         ON
MACM_BFAC,0                     _onoff                         ON
MACM_VRMS,0                     _onoff                         OFF
MACM_LAST,0                     _onoff                         OFF
MACM_NCYC,0                     _positiveint                   50 

#PACK
TOG_PACK                        _logical                       ""
PACK_OPTION                     _packing_option                PERCENT
PACK_ALLOWED_CLASHES            _positiveint                   5
TOG_PACK_QUICK                  _logical                       ""
PACK_QUICK_ONOFF                _onoff                         ON
TOG_PACK_COMPACT                _logical                       ""
PACK_COMPACT_ONOFF              _onoff                         ON
TOG_PACK_DISTANCE               _logical                       ""
PACK_DISTANCE                   _positivereal                  3.0
TOG_PACK_TRACE                  _logical                       ""
PACK_TRACE                      _onoff                         ON

#PEAKS
TOG_FINAL_TRA                   _logical                       0
TOG_FINAL_SIGMA_TRA             _logical                       0
TOG_PEAKS_TRA_CLUSTER           _logical                       0
FINAL_OPTION_TRA                _peaks_option                  PERCENT
FINAL_SIGMA_TRA                 _real                          75
PEAKS_TRA_CLUSTER               _onoff                         ON

#PERM
TOG_PERMUTATIONS                _logical                       0
PERMUTATIONS_ONOFF              _onoff                         OFF

#PURGE
TOG_PURGE_TRA                   _logical                       0
PURGE_TRA_ONOFF                 _onoff                         ON
PURGE_TRA_PERCENT               _positivereal                  75
PURGE_TRA_NUMBER                _positiveint                   ""

#RESCORE
TOG_RESCORE_TRA                 _logical                       0
RESCORE_ONOFF_TRA               _tribool                       NOT_SET

#RESOLUTION
TOG_RESOLUTION                  _logical                       0
RESOLUTION_DMAX                 _positivereal                  ""
RESOLUTION_DMIN                 _positivereal                  ""
RESOLUTION_DMIN_MR              _positivereal                  "" 
TOG_RESOLUTION_AUTO             _logical                       0
RESOLUTION_AUTO_DMAX            _positivereal                  ""
RESOLUTION_AUTO_DMIN            _positivereal                  ""

#ROOT
ROOT                            _text                          ""
FILENAME_ROOT                   _text                          ""

#SEARCH
TOG_SEARCH_METHOD               _logical                       0
SEARCH_METHOD                   _search_method                 FAST
SEARCH_DOWN_PERC                _positivereal                  15
SEARCH_DEEP                     _onoff                         ON

#SOLUTION
# -notoblig must be different parameter name
SET_SOL_FILE_NOTOB              _sol_file                      ""
DIR_SET_SOL_FILE_NOTOB          _default_dirs                  ""

#SPACEGROUP
TOG_SPACEGROUP                  _logical                       0
FILE_SPACEGROUP                 _space_group                   ""
TEST_SPACEGROUP                 _laue_space_group              ""
SPACGROUP_NUMBER                _space_groups                  ""

#SGALTERNATIVE
PHASER_TEST_SG                  _laue_space_group              ""
SPACEGROUP_OPTION               _spacegroup_option             SG_MTZ 
LAUE_SPGP_LIST                  _list_of_text                  ""
LAUE_SPGP_ALIAS                 _list_of_text                  ""

#TITLE
TITLE                           _title_text                    ""

#XYZOUT_NPDB
TOG_TOPF                        _logical                       0
XYZOUT_NPDB                     _positiveint                   1 

#TNCS
TOG_TNCS_USE                    _logical                       0
TNCS_USE                        _onoff                         ON
TNCS_USE_AND_VALID              _logical                       1
TOG_TNCS_NMOL                   _logical                       0
TNCS_NMOL                       _positiveint                   2
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_RESTRAINT         _logical                       0                 
TNCS_LINK_RESTRAINT             _onoff                         ON                
TNCS_LINK_SIGMA                 _real                          ""         
TOG_TNCS_PAIR_ONLY              _logical                       0                 
TNCS_PAIR_ONLY                  _onoff                         ON             

#VERBOSE
TOG_VERBOSE                     _logical                       0

#XYZOUT
TOG_XYZOUT                      _logical                       0
XYZOUT_ONOFF                    _onoff                         ON

#ZSCORE
TOG_ZSCORE                      _logical                       0
ZSCORE_USE                      _onoff                         ON
ZSCORE_SOLVED                   _positivereal                  8
ZSCORE_HALF                     _onoff                         ON
