#CCP4I VERSION CCP4Interface 6.2.0
#CCP4I SCRIPT DEF prosmart
#CCP4I DATE 04/11/11

TITLE						_text					"ProSMART_job"

PRIMARY_MODE                _primary_program_mode   BOTH_
MOLECULE_TYPE               _molecule_type          PROTEIN
SECONDARY_MODE_ALIGN        _secondary_mode_align   STANDARD
SECONDARY_MODE_RESTR        _secondary_mode_restr   STANDARD
SECONDARY_MODE_DNARNA       _secondary_mode_dnarna  STANDARD

OUTPUT_FILES                _list_of_text           "OUTPUTS"
OUTPUTS                     _any_file               ""
DIR_OUTPUTS                 _default_dirs           ""

HIDE_REFERENCE              _logical                0

ALIGN						_logical				1
ALIGN_MODE                  _align_mode             ALL
RESTRAIN                    _logical				1
RESTRAIN_WARNING            _logical				0

USE_HBOND                   _logical				0
USE_DNARNA                  _logical				0

ALL_ON_ALL                  _logical				0
TRIANGULAR                  _logical				0

MENU1,0                     _list					""
MENU2,0                     _list					""

OUT                         _text					"ProSMART_Output"
DIR_OUT                     _dir					""

KEYWORDS                    _any_file               ""
DIR_KEYWORDS                _default_dirs           ""

P1,0						_pdb_file				""
DIR_P1,0                    _default_dirs           ""
NP1							_positiveint            1
C1,0						_target_chains1         ""
NC1,0						_positiveint            1
C1_TYPE                     _chain_type             "ALL"

P2,0						_pdb_file				""
DIR_P2,0                    _default_dirs           ""
NP2							_positiveint            1
C2,0						_target_chains2         ""
NC2,0						_positiveint            1
C2_TYPE                     _chain_type             "ALL"

USE_LIB                     _logical				0
LIB							_logical				0
HELIX						_logical				1
STRAND                      _logical				0
LIB_ADVANCED                _logical				0
LIB_CONFIG                  _any_file               ""
LIB_DIR                     _dir                    ""
LIB_SCORE                   _real                   ""
LIB_FRAGLEN					_positiveint            ""

RANGE_SHOW                  _logical                0
NRANGE1						_positiveint            0
RANGE1PDB,0                 _text                   "ALL"
RANGE1CHAIN,0               _text                   "ALL"
RANGE1A,0                   _int                    ""
RANGE1B,0                   _int                    ""
NRANGE2						_positiveint            0
RANGE2PDB,0                 _text                   "ALL"
RANGE2CHAIN,0               _text                   "ALL"
RANGE2,0                    _text                   ""

RANGE3_SHOW                 _logical                0
NRANGE3						_positiveint            0
RANGE3PDB,0                 _text                   "ALL"
RANGE3CHAIN,0               _text                   "ALL"
RANGE3A,0                   _int                    ""
RANGE3B,0                   _int                    ""
NRANGE4						_positiveint            0
RANGE4PDB,0                 _text                   "ALL"
RANGE4CHAIN,0               _text                   "ALL"
RANGE4,0                    _text                   ""

FRAGLEN_SHOW                _logical                0
FRAGLEN						_positiveint            9
REFINE_ALIGNMENT            _logical                1
SEQUENCE_IDENTICAL          _logical                0     
ADJUST_HELIX                _logical                0
HELIX_SCORE                 _real                   0.2
HELIX_PENALTY               _real                   1.0
ALIGN_SCORE_SHOW            _logical                0
ALIGN_SCORE                 _real                   1.0
REWARD_SEQ_ENABLE           _logical                1
REWARD_SEQ_SHOW             _logical                0
REWARD_SEQ                  _real                   -2.0

SCORE_NCO                   _logical                0
SCORE_FLIP                  _logical                1
SCORE_COSINE                _logical                0

SUBSTRUCTURE_ID             _logical                1
RIGID_SCORE_SHOW            _logical                0
RIGID_SCORE                 _real                   1.0 
RIGID_ANGLE                 _real                   15.0
RIGID_MIN_SHOW              _logical                0
RIGID_MIN                   _positiveint            10
RIGID_LINK_SHOW             _logical                0
RIGID_LINK                  _real                   0.998
RIGID_RIGID                 _real                   0.998
RIGID_COLOUR                _real                   1.0

RESTRAIN_TYPE               _restrain_type          SIDE
RESTRAIN_REFMACTYPE         _restrain_refmactype    EXTERNAL
RESTRAIN_BEST               _logical                1
RESTRAIN_TYPE_SHOW          _logical                0
RESTRAIN_RMAX_SHOW          _logical                0
RESTRAIN_RMAX               _real                   6.0
RESTRAIN_RMIN               _real                   2.5
RESTRAIN_SIGMATYPE          _sigma_type             SIGMA_DEFAULT
RESTRAIN_SCALE              _real                   1.0
RESTRAIN_SIGMA              _real                   0.1
RESTRAIN_SIGMAMIN           _real                   0.01
RESTRAIN_SCORE_SHOW         _logical                0
RESTRAIN_SCORE              _real                   ""
RESTRAIN_SIDE               _real                   ""
RESTRAIN_OUTLIER_SHOW       _logical                0
RESTRAIN_OUTLIER            _real                   ""
RESTRAIN_RMBONDS            _logical                0
RESTRAIN_GENERIC_SELF       _logical                0

HBOND_MODE                  _hbond_mode             ALL
HBOND_SSEMODE               _hbond_ssemode          ALL
HBOND_DISPLAYSSE            _logical                0
HBOND_DISPLAYHELIX          _logical                0
HBOND_DISPLAYCUSTOM         _logical                0
HBOND_3                     _logical                1
HBOND_4                     _logical                1
HBOND_5                     _logical                1
HBOND_STRICT                _logical                0
HBOND_ALTER                 _logical                0
HBOND_TARGET                _real                   2.8
HBOND_MIN                   _real                   2.0
HBOND_MAX                   _real                   3.5
HBOND_MINSEP                _positiveint            3
HBOND_MAXSEP                _positiveint            ""
HBOND_REMOVESEP             _text                   ""
HBOND_OPT                   _hbond_opt              ONNO
HBOND_OVERRIDE              _logical                0
HBOND_OVERRIDE_VAL          _positiveint            ""

OUTPUT_PDB                  _logical                1
OUTPUT_PDB_FULL             _logical                0
SUPERPOSITION_SHOW          _logical                0
SUPERPOSITION_SCORE         _real                   1.0
OUTPUT_EXTRA_RESTRAINTS     _logical                0

OUTPUT_COLOUR               _logical                1
COLOUR_SCORE_SHOW           _logical                0
COLOUR_SCORE                _real                   1.0
COLOUR_SCORE_SIDE           _real                   1.0
COLOUR_SHOW                 _logical                0
COLOUR_D1                   _real                   1.0
COLOUR_D2                   _real                   1.0
COLOUR_D3                   _real                   0.0
COLOUR_S1                   _real                   0.8
COLOUR_S2                   _real                   0.0
COLOUR_S3                   _real                   0.0

THREADS_SHOW                _logical                0
THREADS						_positiveint			4
MERGE						_logical                0
XML                         _logical                0
XML_FILE					_text					"xmlout.txt"
REFMAC_SHOW                 _logical				0
REFMAC                      _text					"refmac5"
EXTRA_KEYWORDS              _text					""
