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

MR_MODE                         _mode_menu                     AUTO
#for backwards compatibility
MR_MODE_SELECT_ROT              _mode_rot                      MR_FRF
MR_MODE_SELECT_TRAN             _mode_tran                     MR_FTF
MR_MODE_SELECT                  _text                          MR_AUTO
#end backwards compatibility
TOG_INTENSITY_OPTION            _logical                       1

#lists for ccp4 input and output files, in scripts/phaser_MR.script
INPUT_FILES                     _list_of_text                  ""
OUTPUT_FILES                    _list_of_text                  ""

#BINS
TOG_BINS                        _logical                       0
BINS_L                          _positiveint                   6
BINS_H                          _positiveint                   50
BINS_W                          _positiveint                   500
TOG_BINS_ENSE                   _logical                       0
BINS_ENSE_L                     _positiveint                   6
BINS_ENSE_H                     _positiveint                   1000
BINS_ENSE_W                     _positiveint                   1000

#BOXSCALE
TOG_BOXSCALE                    _logical                       0
BOXSCALE                        _real                          4

#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

#ELLG
TOG_USE_ELLG                    _logical                       0                 
ELLG_TARGET                     _real                          225             

#ENSEMBLE
N_PDB,0                         _positiveint                   1
XYZIN,0                         _pdb_file                      ""
DIR_XYZIN,0                     _default_dirs                  ""
XYZIN,1_1                       _pdb_file                      ""
DIR_XYZIN,1_1                   _default_dirs                  ""
RMS_OPTION,0                    _rmsid_option                  IDENT
RMS_OPTION,1_1                  _rmsid_option                  IDENT
RMS,0                           _real                          ""
RMS,1_1                         _real                          ""
N_ENSEMBLE                      _positiveint                   1
ENSEMBLE_ID,0                   _text                          ""
ENSEMBLE_ID,1                   _text                          ensemble1
TOG_HETATM,0                    _logical                       0
TOG_HETATM,1                    _logical                       0
ENSEMBLE_MENU_LIST              _ensemble_menu                 ""
ENSEMBLE_OPTION,0               _ensemble_option               PDB
ENSEMBLE_OPTION,1               _ensemble_option               PDB
ENSEMBLE_PROTMW,0               _positiveint                   ""
ENSEMBLE_NUCLMW,0               _positiveint                   ""
HKLIN,0                         _MTZ_file                      ""
HKLIN,1                         _MTZ_file                      ""
DIR_HKLIN,0                     _default_dirs                  ""
DIR_HKLIN,1                     _default_dirs                  ""
HKLIN,1_1                       _MTZ_file                      ""
DIR_HKLIN,1_1                   _default_dirs                  ""
ENSEMBLE_LABIN,0                _text                          "FC PHIC"
FC,0                            _mtz_label_f                   ""
PHIC,0                          _mtz_label_phi                 ""
ENSEMBLE_EXT_X,0                _real                          ""
ENSEMBLE_EXT_Y,0                _real                          ""
ENSEMBLE_EXT_Z,0                _real                          ""
ENSEMBLE_RMS_MTZ,0              _positivereal                  ""
ENSEMBLE_CEN_X,0                _real                          ""
ENSEMBLE_CEN_Y,0                _real                          ""
ENSEMBLE_CEN_Z,0                _real                          ""

#FORMFACTORS
TOG_USE_FORM                    _logical                       0                 
FORMFACTORS                     _formfactors_option            XRAY             

#ENSEMBLE

#HKLIN
HKLIN_MAIN                      _MTZ_file                      ""
DIR_HKLIN_MAIN                  _default_dirs                  ""
F                               _mtz_label_f                   ""
SIGF                            _mtz_label_sig                 ""
I                               _mtz_label_j                   ""
SIGI                            _mtz_label_sig                 ""
FWT                             _mtz_label_f                   ""
PHWT                            _mtz_label_phi                 ""
FMAP                            _mtz_label_f                   ""
PHMAP                           _mtz_label_phi                 ""
FOM                             _mtz_label_w                   ""
TOG_FFWT                        _logical                       1
TOG_FFOM                        _logical                       0

#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

#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                      _logical                       1
MACM_TRA,0                      _logical                       1
MACM_BFAC,0                     _logical                       1
MACM_VRMS,0                     _logical                       0
MACM_CELL,0                     _logical                       0
MACM_LAST,0                     _logical                       0
MACM_NCYC,0                     _positiveint                   50 

#PRUNE
TOG_PRUNE                       _logical                       0
SEARCH_PRUNE                    _onoff                         ON
TOG_OCC2                        _logical                       0
TOG_OCC3                        _logical                       0
OCC_WINDOW                      _occupancy_option              OCCELLG
OCC_ELLG_NRES                   _positiveint                   5
OCC_WINMAX                      _positiveint                   11

#OUTLIER
TOG_OUTLIER                     _logical                       0
OUTLIER_OPTION                  _onoff                         ON
OUTLIER_PROB                    _fraction                      0.000001

#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_KEEP_HIGH_TFZ          _logical                       ""
PACK_KEEP_HIGH_TFZ_ONOFF        _onoff                         OFF
TOG_TRAN_PACK_USE                _logical                      ""
TRAN_PACK_USE                    _onoff                        ON
TRAN_PACK_PERCENT                _positivereal                 50

#PEAKS
TOG_FINAL_ROT                   _logical                       0
TOG_FINAL_SIGMA_ROT             _logical                       0
TOG_PEAKS_ROT_CLUSTER           _logical                       0
FINAL_OPTION_ROT                _peaks_option                  PERCENT
FINAL_SIGMA_ROT                 _real                          ""
PEAKS_ROT_CLUSTER               _onoff                         ON
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                          ""
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                  ""
PURGE_TRA_NUMBER                _positiveint                   ""
TOG_PURGE_ROT                   _logical                       0
PURGE_ROT_ONOFF                 _onoff                         ON
PURGE_ROT_PERCENT               _positivereal                  ""
PURGE_ROT_NUMBER                _positiveint                   ""
TOG_PURGE_RNP                   _logical                       0
PURGE_RNP_ONOFF                 _onoff                         ON
PURGE_RNP_PERCENT               _positivereal                  ""
PURGE_RNP_NUMBER                _positiveint                   ""

#RESCORE
TOG_RESCORE_ROT                 _logical                       0
RESCORE_ONOFF_ROT               _tribool                       NOT_SET
TOG_RESCORE_TRA                 _logical                       0
RESCORE_ONOFF_TRA               _tribool                       NOT_SET

#RESHARPEN
TOG_RESHARPEN                   _logical                       0
RESHARPEN_PERC                  _positivereal                  100

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

#ROOT
ROOT                            _text                          ""
FILENAME_ROOT                   _text                          ""

#ROTATE
BRF_SEARCH_OPTION               _brf_search_option             AROUND
AROUND_ALPHA                    _angle                         0
AROUND_BETA                     _angle                         0
AROUND_GAMMA                    _angle                         0
AROUND_EULER_RANGE              _angle                         10

#SAMPLING
TOG_SAMP_ROT                    _logical                       0
SAMPLING_ROT                    _real                          ""
TOG_SAMP_TRA                    _logical                       0
SAMPLING_TRA                    _real                          ""

#SEARCH
#rotation search
MR_ROT_SEARCH                   _search_type                   SEARCH_SIMPLE    
MR_ROT_SEARCH_ID                _ensemble_menu                 ""
#rotation or search
N_ROT_SEARCH_EXTRA              _positiveint                   1
MR_ROT_SEARCH_ID_EXTRA,0        _ensemble_menu                 ""
#auto simple search
MR_SEARCH                       _search_type                   SEARCH_SIMPLE
N_SIMPLE_SEARCH                 _positiveint                   1 
MR_SIMPLE_ENSEMBLE_ID,0         _ensemble_menu                 ""
MR_SIMPLE_ENSEMBLE_NUM,0        _positiveint                   1
#auto or search
N_SEARCH                        _positiveint                   1 
MR_FIRST_OR_ENSEMBLE_ID,0       _ensemble_menu                 ""
MR_FIRST_OR_ENSEMBLE_NUM,0      _positiveint                   1
N_SEARCH_EXTRA,0                _positiveint                   1
MR_EXTRA_OR_ENSEMBLE_ID,0       _ensemble_menu                 ""
N_SEARCH_EXTRA,1_1              _positiveint                   1
MR_EXTRA_OR_ENSEMBLE_ID,1_1     _ensemble_menu                 ""
#other commands
TOG_SEARCH_ORDER_AUTO           _logical                       ""
SEARCH_ORDER_AUTO_ONOFF         _onoff                         ON
TOG_SEARCH_METHOD               _logical                       0
SEARCH_METHOD                   _search_method                 FAST
SEARCH_DOWN_PERC                _positivereal                  15
TOG_SEARCH_DEEP                 _logical                       ""
SEARCH_DEEP                     _onoff                         ON
TOG_SEARCH_BFAC                 _logical                       ""
SEARCH_BFAC                     _positivereal                  0
TOG_SEARCH_OFAC                 _logical                       ""
SEARCH_OFAC                     _positivereal                  1
TOG_ROTREF                      _logical                       0
ROTREF                          _onoff                         OFF

#SOLPARAMETERS
TOG_SOLP                        _logical                       ""
TOG_BULK_SOLP                   _logical                       ""
SOLP_FSOL                       _real                          0.69
SOLP_BSOL                       _real                          380
SOLP_SIGA_MIN                   _positivereal                  0.1
SOLP_BULK_FSOL                  _real                          0.35
SOLP_BULK_BSOL                  _real                          45
SOLP_BULK_USE                   _onoff                         OFF 

#SOLUTION
TRA_RLIST_FILE                  _rlist_file                    ""
DIR_TRA_RLIST_FILE              _default_dirs                  ""
SET_SOL_FILE                    _sol_file                      ""
DIR_SET_SOL_FILE                _default_dirs                  ""
# -notoblig must be different parameter name
SET_SOL_FILE_NOTOB              _sol_file                      ""
DIR_SET_SOL_FILE_NOTOB          _default_dirs                  ""
#known pdb search
MR_SOLUTION_MODE_NOTOB          _solution_menu                 SOLNONE 
ORIGIN_SOLUTION_ID_NOTOB        _ensemble_menu                 ""

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

#SGALTERNATIVE
N_SG                            _positiveint                   1
PHASER_TEST_SG,0                _laue_space_group              ""
SPACEGROUP_OPTION               _spacegroup_option             SG_ENANT 
LAUE_SPGP_LIST                  _list_of_text                  ""
LAUE_SPGP_ALIAS                 _list_of_text                  ""
TOG_SGAL_SORT                   _logical                       ""
SGAL_SORT_ONOFF                 _onoff                         ON

#PTGROUP
TOG_PTGR_SEQ                    _logical                       ""
TOG_PTGR_XYZ                    _logical                       ""
PTGR_COVERAGE                   _real                          0.90
PTGR_IDENTITY                   _real                          0.95
PTGR_RMSD                       _real                          1.0
PTGR_TOL_ANG                    _real                          0.035
PTGR_TOL_SPC                    _real                          0.5

#TARGET
TOG_FRF_TARGET                  _logical                       0
FRF_TARGET_OPTION               _frf_target_option             FAST
TOG_FTF_TARGET                  _logical                       0
FTF_TARGET_OPTION               _ftf_target_option             FAST
TOG_FRF_TARGET_TYPE             _logical                       0
FRF_TARGET_TYPE_OPTION          _frf_target_type_option        LERF1
TOG_FTF_TARGET_TYPE             _logical                       0
FTF_TARGET_TYPE_OPTION          _ftf_target_type_option        LETF1

#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_TRAN_PERT              _logical                       0
TNCS_TRAN_PERT                  _onoff                         ON
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             

#TRANSLATE
BTF_SEARCH_OPTION               _btf_search_option             AROUND
START_X                         _real                          0
START_Y                         _real                          0
START_Z                         _real                          0
END_X                           _real                          1
END_Y                           _real                          1
END_Z                           _real                          1
COORD_SYS                       _coord_option                  FRAC
AROUND_COORD_RANGE              _real                          10

#VERBOSE
TOG_VERBOSE                     _logical                       0

#XYZOUT
TOG_XYZOUT                      _logical                       0
XYZOUT_ONOFF                    _onoff                         ON

#ZSCORE
TOG_ZSCORE                      _logical                       0
TOG_ZSCORE_SOLVED               _logical                       0
TOG_ZSCORE_STOP                 _logical                       0
TOG_ZSCORE_HALF                 _logical                       0
ZSCORE_USE                      _onoff                         ON
ZSCORE_SOLVED                   _positivereal                  8
ZSCORE_HALF                     _onoff                         ON
ZSCORE_STOP                     _onoff                         OFF
