#
#     Copyright (C) 1999-2004  Liz Potterton, Peter Briggs
#
#     This code is distributed under the terms and conditions of the
#     CCP4 licence agreement as `Part 1' (Annex 2) software.
#     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: refmac5.def,v 1.15 2004/05/14 09:50:38 pjx Exp $
#CCP4I VERSION CCP4Interface 0.2
#CCP4I SCRIPT DEF loopy
#CCP4I DATE  26/06/06 16:05:30
#CCP4I USER kristaj
TITLE           _title_text             ""

MAP_INPUT_MODE			_map_input_mode		MTZ
MODE_LOOPY                      _mode_loopy             0
REFINEMENT			_logical		1

# For the CConfig class:
MESSAGE_FILENAME 		_log_file		"loopy.msg"
DIR_MESSAGE_FILENAME		_default_dirs		""
XML_MESSAGE_FILENAME 		_xml_file 		"loopy.xml"
DIR_XML_MESSAGE_FILENAME	_default_dirs		""
ABORT_LEVEL 			_positiveint 		8
MESSAGE_LEVEL			_positiveint 		5

SPACEGROUP			_space_group		""
SPACEGROUP_NUMBER		_positiveint		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		""

CHECK_FIRST_ANGLE		_logical		1

C_ANCHOR			_loopy_cterm_menu	""
N_ANCHOR			_loopy_nterm_menu	""
MAX_LOOP_LENGTH                 _positiveint            15
LOOP_LENGTH                     _positiveint            0
EXTEND_GAP_SMALLER_THAN		_positiveint		5
USE_PIR_FILE			_logical		1
LOOP_SEQUENCE			_text			""
LOOP_BOTH_WAYS			_logical		1
LOOP_TO_C			_logical		1
LOOP_OVERLAP			_positiveint		0
LOOPS_TO_BUILD			_text			""

LOOP_RMS			_positivereal		0.5
LOOP_DENSITY_CUTOFF_NO		_int			100
LOOP_STRUCTURE_THRESHOLD	_negativereal		-7
LOOP_STRUCTURE_CUTOFF_NO	_int			-1
LOOP_STRUCTURE_MIN_NO		_positiveint		0
MAX_LOOPS_AFTER_MC_PLANE	_int			50
LOOP_MAIN_CHAIN_DENS_NO		_int			12

MAX_DISTANCE_BETWEEN_ANCHORS	_real			-1.

LIKELIHOOD_THRESHOLD		_real			-5
SHOW_DETAILS_LIKELIHOOD		_logical		0
WEIGHT_DISTANCE			_real			1.
WEIGHT_DENSITY			_real			1.
WEIGHT_STRUCTURE		_real			1.
STRUCTURE_TO_C			_any_file		"$warpbin/set_1200_2C_my_0.3b_cos_log.llh"
DIR_STRUCTURE_TO_C		_default_dirs		"Full path.."
STRUCTURE_TO_N			_any_file		"$warpbin/set_1200_2N_my_0.3b_cos_log.llh"
DIR_STRUCTURE_TO_N		_default_dirs		"Full path.."
MINIMAL_DISTANCE		_positivereal		0.45
USER_SETTING_MAX_NO_CAS		_logical                0
MAX_NO_CAS_KEPT			_positiveint		5
FORCE_MIN_CAS_KEPT		_positiveint		1

CA_DISTANCE			_positivereal		3.8
CA_DISTANCE_ERROR		_positivereal		0.3
GRID_TYPE			_loopy_grid_type	0
SHELL_THICKNESS			_positivereal		1
GRID_NUMBER			_positiveint		378
KEEP_NEG_DENS_HALFWAY		_logical		0

FITTARGET			_loopy_fit_target	1
B_FACTOR			_b_value		20
B_FACTOR_SIDE_CHAIN		_b_value		26
ATOM_RADIUS			_positivereal		0.74
REMOVAL_FACTOR			_positivereal		1.
DUMMY_REMOVAL_THRESHOLD		_real			0.1
OVERLAP_REMOVAL_THRESHOLD	_real			0.1

PDB_INPUT_FILENAME		_pdb_file		""
DIR_PDB_INPUT_FILENAME		_default_dirs		""
MAP_FILENAME			_map_file		""
DIR_MAP_FILENAME		_default_dirs		""
EXT_MAP_FILENAME		_map_file		""
DIR_EXT_MAP_FILENAME		_default_dirs		TEMPORARY
INCLUDE_CHAINS                  _text			""
INCLUDE_ALL			_logical		1

MTZ_FILENAME			_MTZ_file		""
DIR_MTZ_FILENAME		_default_dirs		""
MAP_FROM_MTZ			_map_file		""
DIR_MAP_FROM_MTZ		_default_dirs		TEMPORARY

NSEQFILES			_positiveint		1
SEQIN,0				_pir_file		""
DIR_SEQIN,0			_default_dirs		""
MET_IS_SEL,0    		_meth_is_seleno		"0"
NMOL,0				_nmol_int		1
NRESMOL,0			_positiveint		""
NRES,0				_positiveint		""
SEQIN,1				_pir_file		""
DIR_SEQIN,1			_default_dirs		""
MET_IS_SEL,1			_meth_is_seleno		"0"
NMOL,1				_nmol_int		1
NRESMOL,1			_positiveint		""
NRES,1				_positiveint		""

SAVE_BEST_NUMBER		_positiveint		5
SAVE_LOOPS			_logical		1
DIR_SAVE_LOOP_NAME		_default_dirs		""
SAVE_LOOP_NAME			_pdb_file		""
SAVE_LOOP_DIR			_text			""
SAVE_LOOP_BASENAME		_text			""
DIR_SAVE_PROP_PDB		_default_dirs		""
SAVE_PROP_PDB			_pdb_file		""
DIR_OUTPUT_PDB			_default_dirs		""
OUTPUT_PDB			_pdb_file		""
SAVE_LOOP_PROP_DIR		_text			""
SAVE_LOOP_PROP_BASE		_text			""

F1				_mtz_label_f		""
PHI				_mtz_label_phi		""

#refinement
EXTEND_REFINEMENT		_positiveint		0
LOOPFIT_EXE_FILENAME 		_loopfit_exe		"$warpbin/loopfit"
DIR_LOOPFIT_EXE_FILENAME	_warpbin_dir		"Full path.."
LOOPFIT_LOG_FILENAME		_log_file		"loopfit.log"
DIR_LOOPFIT_LOG_FILENAME	_default_dirs		TEMPORARY
PRELOOPFIT_PDB			_pdb_file		"pre_loopfit.pdb"
DIR_PRELOOPFIT_PDB		_default_dirs		TEMPORARY


SHOW_DETAILS_DENSITY		_logical		0
SHOW_PRUNING_DETAILS		_logical		0