#
#     Copyright (C) 1999-2004  Liz Potterton, Peter Briggs
#
#     This code is distributed under the terms and conditions of the
#     CCP4 Program Suite Licence Agreement as a CCP4 Library.
#     A copy of the CCP4 licence can be obtained by writing to the
#     CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK.
#
#CCP4i_cvs_Id $Id$
#CCP4I VERSION CCP4Interface 0.2
#CCP4I SCRIPT DEF refmac
#CCP4I DATE  25/06/97 16:05:30
#CCP4I USER lizp
TITLE           _title_text             ""

INPUT_FILES     _list_of_text           "HKLIN XYZIN"
OUTPUT_FILES    _list_of_text           "HKLOUT XYZOUT"

RESIDUAL        _refmac_residual        MLKF
REFINE_TYPE     _refmac_refine_type     REST
MINIMISATION    _refmac_minimisation    CDIR

ADD_HYDROGENS   _logical                0

EXCLUDE_RESOLUTION      _logical        0
EXCLUDE_RESOLUTION_MIN  _positivereal   ""
EXCLUDE_RESOLUTION_MAX  _positivereal   ""

INPUT_PHASE     _refmac_input_phase     NO
PHASE_SCBLUR    _real                   1.0
PHASE_BBLUR     _real                   0.0

HKLIN           _MTZ_file               ""
DIR_HKLIN       _default_dirs           ""
HKLOUT          _MTZ_file               ""
DIR_HKLOUT      _default_dirs           ""

XYZIN           _pdb_file               ""
XYZOUT          _pdb_file               ""
DIR_XYZIN       _default_dirs           ""
DIR_XYZOUT      _default_dirs           ""

IF_MAPOUT       _logical                0
MAPOUT_FORMAT   _map_format             MAP_DEFAULT
EXTEND_MAP      _logical                1
MAP_BORDER              _positivereal           5.0

PROTIN_PARAMS   _refmac_protin_params   ""
PROTIN_DEF      _def_file               ""
DIR_PROTIN_DEF  _default_dirs           ""
PROTOUT         _data_file              ""
DIR_PROTOUT     _default_dirs           TEMPORARY
PROTCOUNTS      _data_file              ""
DIR_PROTCOUNTS  _default_dirs           TEMPORARY


LABIN           _text           "FP SIGFP"
FP              _mtz_label_f            ""
SIGFP           _mtz_label_sig          ""
PHIB            _mtz_label_phi          ""
FOMB            _mtz_label_w            ""
HLA             _mtz_label_hl           ""
HLB             _mtz_label_hl           ""
HLC             _mtz_label_hl           ""
HLD             _mtz_label_hl           ""

NPARTIALS       _positiveint            0
FPART,0         _mtz_label_f            ""
PHIP,0          _mtz_label_sig          ""
PARTIAL_SCALE,0 _positivereal           1.0

FC              _mtz_label_out          FC
FWT             _mtz_label_out          FWT
PHIC            _mtz_label_out          PHIC
PHWT            _mtz_label_out          PHWT
DELFWT          _mtz_label_out          DELFWT
PHDELWT         _mtz_label_out          PHDELWT
FOM             _mtz_label_out          FOM
PHCOMB          _mtz_label_out          PHCOMB
LABOUT          _text           "FC FWT PHIC PHWT DELFWT PHDELWT FOM"
CTYPOUT         _text                   "F Q P Q F P Q"

TITLE                   _text           ""

SPACE_GROUP             _space_group    ""
CELL_1                  _cell_length    ""
CELL_2                  _cell_length    ""
CELL_3                  _cell_length    ""
CELL_4                  _cell_angle     ""
CELL_5                  _cell_angle     ""
CELL_6                  _cell_angle     ""

NCYCLES                 _positiveint    5
EXTERNAL_NCYCLES        _positiveint    1
B_REFINEMENT            _logical        1
B_REFINEMENT_MODE       _refmac_b_refinement    ISOT

SPLIT_MODE              _refmac_split_mode      BINS
SPLIT_BINS              _positiveint            20
SPLIT_RANGES            _positivereal           0.1

BLIM                    _logical        0
BLIM_MIN                _positivereal   2.0
BLIM_MAX                _positivereal   1000.0

DAMP                    _logical        0
DAMP_P                  _positivereal   0.5
DAMP_B                  _positivereal   0.5

EXCLUDE_FREER           _logical        1
EXCLUDE_FREER_VALUE     _int            0
FREE                    _mtz_label_freer     ""

BULK_SOLVENT_SCALING    _refmac_scaling         BULK
SCALING_RESOLUTION_MIN  _resolution             ""
SIMPLE_SCALING_RESOLUTION_MAX  _resolution      4.5
BULK_SCALING_RESOLUTION_MAX  _resolution        0.0
SCALING_ANISO           _logical                1
SCALING_IF_BAVERAGE     _logical                0
SCALING_BAVERAGE        _positivereal           ""
SCALING_IF_FIXB         _logical                0
SCALING_FIXB_BBULK      _positivereal           70.0
SCALING_FIXB_SCBULK     _positivereal           -0.75
SCALING_NCYCYLES        _positiveint            10
SCALING_EXPE_SIGMA      _logical                1
SCALING_REF_SET         _refmac_ref_set         working
SCALING_APPLY           _refmac_scaling_appl    observed

MLSC_ON                 _logical                0
MLSC_NCYCLES            _positiveint            10
MLSC_IF_FIXB            _logical                0
MLSC_FIXB_BBULK         _positivereal           100.0
MLSC_FIXB_SCBULK        _positivereal           -0.1
MLSC_REF_SET            _refmac_ref_set         free

EXPERIMENTAL_WEIGHTING  _logical                1
WEIGHTING_METHOD        _refmac_weighting       matrix
MATRIX_WEIGHT           _positivereal           0.5
GRADIENT_WEIGHT         _real                   1.0
SIGMA_WEIGHT            _positivereal           0.5

RIGID_NCYCLES           _positiveint            20
INITIALISE_RIGID        _logical                0
NDOMAINS                _positiveint            0
NGROUPS,0               _positiveint            1
CHAIN1,0                _chain_id               ""
RES1,0                  _res_id                 ""
RES2,0                  _res_id                 ""
TRANS_ON,0              _logical                0
TRANS_X,0               _real                   ""
TRANS_Y,0               _real                   ""
TRANS_Z,0               _real                   ""
EULER_ON,0              _logical                0
EULER_ALPHA,0           _real                   ""
EULER_BETA,0            _real                   ""
EULER_GAMMA,0           _real                   ""
EXCLUDE_ATOMS,0         _refmac_rigid_exclude   no

MONI_LEVEL              _refmac_monitor_level   few
RIGID_MONI_LEVEL        _refmac_rigid_monitor_level     few
MONI_MODE               _refmac_monitor_mode    "N*Sigma"
MONI_HBOND              _logical                0

MONI_BADTOR             _positivereal           3.0
MONI_BADDIS             _positivereal           3.0
MONI_BADPLN             _positivereal           3.0
MONI_BADVDW             _positivereal           0.6

MONI_BADSHI             _positivereal           0.4
MONI_CHIRAL             _positivereal           2.5

MONI_TORCUT             _positivereal           5.0
#MONI_CHICUT            _positivereal           
MONI_DSCUT              _positivereal           5.0
MONI_PLCUT              _positivereal           5.0
MONI_VDWCUT             _positivereal           0.6

MONI_IHYDP              _positivereal           2.0
MONI_DBCUT              _positivereal           0.25

IFDIST                  _logical                0
IFPLAN                  _logical                0
IFCHIR                  _logical                0
IFTMP                   _logical                0
IFNCSR                  _logical                0
IFTORS                  _logical                0
IFVAND                  _logical                0
IFHOLD                  _logical                0

WDSKAL          _positivereal           1.0
SIGD1           _positivereal           0.02
SIGD2           _positivereal           0.04
SIGD3           _positivereal           0.05
SIGD4           _positivereal           0.05
SIGD5           _positivereal           0.02

WPSKAL          _positivereal           1.0
SIGPP           _positivereal           0.03
SIGPA           _positivereal           0.02

WCSKAL          _positivereal           1.0
SIGC            _positivereal           0.15

WBSKAL          _positivereal           1.0
SIGB1           _positivereal           2.0
SIGB2           _positivereal           3.0
SIGB3           _positivereal           2.0
SIGB4           _positivereal           3.0

WSSKAL          _positivereal           1.0
SIGSP1          _positivereal           0.05
SIGSP2          _positivereal           0.5
SIGSP3          _positivereal           5.0
SIGSB1          _positivereal           0.5
SIGSB2          _positivereal           2.0
SIGSB3          _positivereal           10.0

WTSKAL          _positivereal           1.0
SIGT1           _positivereal           15.0
SIGT2           _positivereal           3.0
SIGT3           _positivereal           15.0
SIGT4           _positivereal           20.0

WVSKAL          _positivereal           1.0
SIGV            _positivereal           1.0
DINC1           _real                   -0.3
DINC2           _real                   0.0
DINC3           _real                   0.0

PBEL            _positivereal           0.3
BDEL            _positivereal           3.0
QDEL            _positivereal           0.2

SPHERICITY      _real                   5.0
RBOND           _real                   1.0


RUN_ARP                 _logical                0
ARP_UPDATE_MODE         _arp_refine_mode       WATERS
ARP_REFINE_MODE         _arp_refine_mode       WATERS
INPUT_XYZLIM            _logical                0
XYZLIM_1                _real                   ""
XYZLIM_2                _real                   ""
XYZLIM_3                _real                   ""
XYZLIM_4                _real                   ""
XYZLIM_5                _real                   ""
XYZLIM_6                _real                   ""
ARP_REMOVE              _logical                1
ARP_FIND                _logical                1
ARP_REFINE              _logical                1
FIND_ATOMS              _positiveint            ""
FIND_CHAIN              _text                   W
FIND_CUTSIGMA           _real                   ""
FIND_CUTSIGMA_AUTO      _text                   AUTO
REMOVE_ATOMS            _positiveint            25
REMOVE_CUTSIGMA         _positivereal           "0.5"
REMOVE_MERGE            _logical                1
REMOVE_MERGE_CUTOFF_WAT     _positivereal           2.2
REMOVE_MERGE_CUTOFF_ALL     _positivereal           0.6

FIND_NEWOLD_MIN         _positivereal           2.2
FIND_NEWOLD_MAX         _positivereal           3.3
FIND_NEWNEW             _positivereal           2.2

FDISTANCE               _logical                1

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