#CCP4I VERSION CCP4Interface 1.0
#CCP4I SCRIPT DEF crank2
#CCP4I DATE 02/27/04
#CCP4I USER raj

#                     General CCP4i setup                      

# Title of Crank run
VERSION                         		_text               		"2.0.160"
TITLE						_text               		""

# Global Crank input and output files 
INPUT_FILES                     		_list_of_text       		"HKLIN XYZIN COORDSIN"
EXPERT                                          _logical                        0
ONE_MTZ                 			_logical    			0
REFL_TYPE                 			_text    			"MTZ"
HKLIN                           		_MTZ_file           		""
DIR_HKLIN                       		_default_dirs       		""
XYZIN	                          		_pdb_file           		""
DIR_XYZIN	                      		_default_dirs       		""
SEQUENCE					_text				""
SEQIN                           		_seq_file           		""
DIR_SEQIN                      	 		_default_dirs       		""
OUTPUT_FILES                    		_list_of_text       		"XYZOUT LOGGRAPH_FILE LOGGRAPHACT_FILE"
XYZOUT                          		_pdb_file           		""
DIR_XYZOUT                      		_default_dirs       		""
LOG_FILE              				_log_file               	""
LOGGRAPH_FILE                           _log_graph_file         ""
LOGGRAPHACT_FILE                        _log_graph_file         ""
DIR_LOGGRAPH_FILE                       _default_dirs           ""
DIR_LOGGRAPHACT_FILE                    _default_dirs           ""

EXPERIMENT_SETUP                		_experiment_setup   		"SAD"

# Required parameters
BFACTOR                         		_positivereal       		""
SOLVENT_CONTENT                 		_positivereal       		""
USER_SOLVENT_CONTENT                 	_positivereal       		""
NRESIDUES                       		_positiveint        		""
NNUCLEOTIDES                    		_positiveint        		""
NUCLEOTIDES_PRESENT             		_logical           		0
NMONOMERS					_positiveint	    		""
USER_NMONOMERS				_positiveint	    		""
MATTHEWS					_positivereal	    		""
KRPROB 						_positivereal	    		""

# Input Space group name and number - space group can change during run
# 
SPACE_GROUP_NAME                		_positiveint        		""
SPACE_GROUP_NUMBER              		_positiveint        		""

SHOW_ALL_PIPELINE_INPUT         		_logical            		0
DOCK_SEQUENCE                   		_logical            		1
PARTIAL_MODEL					_partial_model			"NO"
PARTIAL_AS_SUBSTR				_logical            		0
NOT_SEPAR_PARTIAL			         _logical            		0
SKIP_HAND			         _logical            		0
FREE_LABEL	                      		_mtz_label_freer                "Unassigned"
INPUT_FREE		                	_logical			0
NEW_FREE		                	_logical			0
IS_FREE		                	_logical			0

N_CRYSTALS  					_positiveint        		0
CRYSTAL_ID,0 					_text               		""
CRYSTAL_NATIVE,0    				_logical            		0
CRYSTAL_ATOM_NAME,0				_text               		""
CRYSTAL_N_ATOMS,0				_positiveint        		""
USER_CRYSTAL_N_ATOMS,0				_positiveint        		""
CRYSTAL_ASU_ATOMS,0				_positiveint        		""
CRYSTAL_INPUT_SUBSTRUCTURE,0 			_logical			0
CRYSTAL_INPUT_SUBSTRUCTURE,1 			_logical        		0
CRYSTAL_INPUT_SUBSTRUCTURE_TYPE,0 		_substructure_input_type        "Pdb"
CRYSTAL_INPUT_SUBSTRUCTURE_TYPE,1 		_substructure_input_type        "Pdb"
COORDINATE_FORMAT,0 				_coordinate_format_type         "Fractional"
COORDINATE_FORMAT,1 				_coordinate_format_type         "Fractional"
SUBSTRUCTURE_INPUT_COORDSIN,0 			_pdb_file           		""
DIR_SUBSTRUCTURE_INPUT_COORDSIN,0   		_default_dirs       		""

# Cell dimensions - will change to allow different cells for different
# data sets
CELL_1                            		_positivereal       		""
CELL_2                            		_positivereal       		""
CELL_3                            		_positivereal       		""
CELL_4                            		_positivereal       		""
CELL_5                            		_positivereal       		""
CELL_6                            		_positivereal       		""
CELL_A,0                          		_positivereal       		""
CELL_B,0                          		_positivereal       		""
CELL_C,0                          		_positivereal       		""
CELL_ALPHA,0                      		_positivereal       		""
CELL_BETA,0                       		_positivereal       		""
CELL_GAMMA,0                      		_positivereal       		""

# DATA 

N_DATA,0                        		_positiveint        		0
N_DATA,1                        		_positiveint        		0

# This is calculated by crank_run and is the total number of
# all datasets in all crystals.
TOTAL_DATASETS                  		_positiveint        		0

# Variables describing each dataset
SCAIN,0                       			_sca_file           		""
DIR_SCAIN,0                   			_default_dirs       		""
SCAIN,1_1                       		_sca_file           		""
DIR_SCAIN,1_1                   		_default_dirs       		""
MTZIN,0                       			_MTZ_file           		""
DIR_MTZIN,0                   			_default_dirs       		""
MTZIN,1_1                       		_MTZ_file           		""
DIR_MTZIN,1_1                   		_default_dirs       		""
DATA_ID,0 	                    		_text	          		""
DATA_ID,1_1     	              		_text	          		""
DATA_TYPE,0                     		_data_type          		PEAK
DATA_TYPE,1_1                   		_data_type          		PEAK
DATA_WAVELENGTH,0              	 		_positivereal       		""
DATA_WAVELENGTH,1_1             		_positivereal       		""
DATA_ANOMALOUS,0                		_logical            		1
DATA_ANOMALOUS,1_1              		_logical            		1
SEPARATE_MTZIN,0                       			_logical           		0
SEPARATE_MTZIN,1_1                       		_logical           		0
INPUT_DATA,0                              	_data_input_type                "Intensities"
INPUT_DATA,1_1                             	_data_input_type                "Intensities"
INPUT_INTENSITY,0                           	_logical                1
INPUT_INTENSITY,1_1                          	_logical                1

# Variables of dataset and atom

N_WATOMS,0					_positiveint			1
N_WATOMS,1					_positiveint			1
N_WATOMS,1_1					_positiveint			1
ATOM_WAVE_ID1,0					_text				""
ATOM_WAVE_ID1,1_1				_text				""
ATOM_WAVE_ID2,0					_text				""
ATOM_WAVE_ID2,1_1				_text				""
ATOM_WAVE_ID3,0					_text				""
ATOM_WAVE_ID3,1_1				_text				""
ATOM_WAVE_ID4,0					_text				""
ATOM_WAVE_ID4,1_1				_text				""
ATOM_WAVE_ID5,0					_text				""
ATOM_WAVE_ID5,1_1				_text				""
ATOM_WAVE_ID6,0					_text				""
ATOM_WAVE_ID6,1_1				_text				""
DATA_FPRIME1,0                   		_real       			""
DATA_FPRIME1,1_1                 		_real       			""
DATA_FPRIME2,0                   		_real       			""
DATA_FPRIME2,1_1                 		_real       			""
DATA_FPRIME3,0                   		_real       			""
DATA_FPRIME3,1_1                 		_real       			""
DATA_FPRIME4,0                   		_real       			""
DATA_FPRIME4,1_1                 		_real       			""
DATA_FPRIME5,0                   		_real       			""
DATA_FPRIME5,1_1                 		_real       			""
DATA_FPRIME6,0                   		_real       			""
DATA_FPRIME6,1_1                 		_real       			""
DATA_FPRIMEPRIME1,0              		_positivereal       		""
DATA_FPRIMEPRIME1,1_1            		_positivereal       		""
DATA_FPRIMEPRIME2,0              		_positivereal       		""
DATA_FPRIMEPRIME2,1_1            		_positivereal       		""
DATA_FPRIMEPRIME3,0              		_positivereal       		""
DATA_FPRIMEPRIME3,1_1            		_positivereal       		""
DATA_FPRIMEPRIME4,0              		_positivereal       		""
DATA_FPRIMEPRIME4,1_1            		_positivereal       		""
DATA_FPRIMEPRIME5,0              		_positivereal       		""
DATA_FPRIMEPRIME5,1_1            		_positivereal       		""
DATA_FPRIMEPRIME6,0              		_positivereal       		""
DATA_FPRIMEPRIME6,1_1            		_positivereal       		""

# Intensity columns 
DATA_I,0                        		_mtz_label_j        		""
DATA_I,1_1                      		_mtz_label_j        		""
DATA_SIGI,0                     		_mtz_label_sig      		""
DATA_SIGI,1_1                   		_mtz_label_sig      		""
DATA_I_PLUS,0                   		_mtz_label_k        		""
DATA_I_PLUS,1_1                 		_mtz_label_k        		""
DATA_SIGI_PLUS,0               			_mtz_label_m        		""
DATA_SIGI_PLUS,1_1              		_mtz_label_m        		""
DATA_I_MINUS,0                  		_mtz_label_k        		""
DATA_I_MINUS,1_1                		_mtz_label_k        		""
DATA_SIGI_MINUS,0               		_mtz_label_m        		""
DATA_SIGI_MINUS,1_1             		_mtz_label_m        		""

# Amplitude columns
DATA_F,0                        		_mtz_label_f        		""
DATA_F,1_1                      		_mtz_label_f        		""
DATA_SIGF,0                     		_mtz_label_sig      		""
DATA_SIGF,1_1                   		_mtz_label_sig      		""
DATA_F_PLUS,0                   		_mtz_label_g        		""
DATA_F_PLUS,1_1                 		_mtz_label_g        		""
DATA_SIGF_PLUS,0               			_mtz_label_l        		""
DATA_SIGF_PLUS,1_1              		_mtz_label_l        		""
DATA_F_MINUS,0                  		_mtz_label_g        		""
DATA_F_MINUS,1_1                		_mtz_label_g        		""
DATA_SIGF_MINUS,0               		_mtz_label_l        		""
DATA_SIGF_MINUS,1_1             		_mtz_label_l        		""

# HL columns
HLA						_mtz_label_hl                   ""
HLB						_mtz_label_hl                   ""
HLC						_mtz_label_hl                   ""
HLD						_mtz_label_hl                   ""

# Atom

NUM_ATOMS,0               			_positiveint            	0
NUM_ATOMS,1               			_positiveint            	0
N_ATOMS,0               			_positiveint            	1
N_ATOMS,1               			_positiveint            	1
ATOM_ID,0               			_text                   	""
ATOM_ID,1_1             			_text                   	""
ATOM_SITE,0             			_positiveint            	""
ATOM_SITE,1_1   				_positiveint                    ""
ATOM_X,0                			_real           		""
ATOM_Y,0                			_real           		""
ATOM_Z,0                			_real           		""
ATOM_X_NOREF,0 					_logical			0
ATOM_Y_NOREF,0 					_logical                        0
ATOM_Z_NOREF,0 					_logical                        0
ATOM_X,1_1              			_real           		""
ATOM_Y,1_1              			_real           		""
ATOM_Z,1_1              			_real           		""
ATOM_X_NOREF,1_1        			_logical                	0
ATOM_Y_NOREF,1_1        			_logical                	0
ATOM_Z_NOREF,1_1        			_logical                	0
ATOM_OCCU,0             			_positivereal           	0.5
ATOM_BISO,0             			_positivereal           	""
ATOM_OCCU_NOREF,0       			_logical                	0
ATOM_BISO_NOREF,0       			_logical                	0
ATOM_UANO_NOREF,0       			_logical                	0
ATOM_U11,0              			_positivereal           	""
ATOM_U12,0              			_positivereal           	""
ATOM_U13,0              			_positivereal           	""
ATOM_U22,0              			_positivereal           	""
ATOM_U23,0              			_positivereal           	""
ATOM_U33,0              			_positivereal           	""
ATOM_OCCU,1_1           			_positivereal           	0.5
ATOM_BISO,1_1           			_positivereal           	""
ATOM_OCCU_NOREF,1_1     			_logical                	0
ATOM_BISO_NOREF,1_1     			_logical                	0
ATOM_UANO_NOREF,1_1     			_logical                	0
ATOM_U11,1_1            			_positivereal           	""
ATOM_U12,1_1            			_positivereal           	""
ATOM_U13,1_1            			_positivereal           	""
ATOM_U22,1_1            			_positivereal           	""
ATOM_U23,1_1            			_positivereal           	""
ATOM_U33,1_1            			_positivereal           	""
ISOTROPIC_B,0           			_logical               	 	1
ISOTROPIC_B,1_1         			_logical                	1

#                 Program flow and data passing                
#                                                              
# This section holds general information about the programs to 
# run and the information that is passed between the programs. 
#                                                              

N_PROCESS	                      		_positiveint        		0
PROCESS_NAME,0                  		_text               		""
PROCESS_STEP,0					_positiveint	    		""

# Currently selected program
EXPERIMENTAL_PROCESS            		_pipeline_step   	 	"detect"
PREMADE_START	                		_pipeline_start       		"Substructure detection"
PREMADE_END	                		_pipeline_step       		"Model refinement"
DISPLAY_PIPELINE	               		_logical            		0
GENERIC_KEYWORDS,0				_title_text			""
GENERIC_KEYWORDS,1_1				_title_text			""
GENERIC_N_KEYWORDS,0				_positiveint			0
REFINE_PROGRAMS,0				_refine_progs			""
REFINE_PROGRAMS,1_1				_refine_progs			""
DETECT_PROGRAMS,0				_detect_progs			""
DETECT_PROGRAMS,1_1				_detect_progs			""
PEAK_PROGRAMS,0					_peak_progs			""
PEAK_PROGRAMS,1_1				_peak_progs			""
PHASING_PROGRAMS,0				_phase_progs			""
PHASING_PROGRAMS,1_1			_phase_progs			""
HAND_PROGRAMS,0					_key_hand_progs			""
HAND_PROGRAMS,1_1				_key_hand_progs			""
DM_PROGRAMS,0					_key_dm_progs			""
DM_PROGRAMS,1_1					_key_dm_progs			""
BUILD_PROGRAMS,0				_key_build_progs		""
BUILD_PROGRAMS,1_1				_key_build_progs		""
DEFAULTS_SET		               	_logical			0

FA_PROGRAM,0					_fa_progs			""
DETECT_PROGRAM,0				_detect_progs			""
DETECT_MANUAL_RESO,0				_logical			""
DETECT_HIGHRES_CUTOFF,0				_positivereal			""
DETECT_NUM_CYCLES,0				_positiveint			""
DETECT_SPECIAL_POSITIONS,0			_logical			""
DETECT_PATTERSON,0				_logical			""
DETECT_THRESHOLD_SHELX,0				_positivereal			""
DETECT_THRESHOLD_CRUNCH,0				_positivereal			""
PEAK_PROGRAM,0					_peak_progs				""
PEAK_THRESHOLD,0				_positivereal			""
PEAK_CYCLES,0					_positiveint			""
PHASING_PROGRAM,0				_phase_progs			""
PHASING_CYCLES,0				_positiveint			""
HAND_DM_PROGRAM,0					_hand_progs				""
HAND_DM_CYCLES,0					_positiveint			""
HAND_PHASE_COMB_PROGRAM,0			_hand_phase_comb_progs		""
PHASE_COMB_PROGRAM,0				_phase_comb_progs		""
DM_PROGRAM,0					_dm_progs				""
DM_CYCLES,0					_positiveint				""
# not really logical as "None" means True (suppresed for 1 monomer only), thus the default of 1
DM_NCS_PARROT,0					_logical				1
BUILD_CYCLES,0					_positiveint			""
BUILD_CYCLES_MAX,0					_positiveint			""
BUILD_CYCLES_MIN,0					_positiveint			""
BUILD_SKIP_INIT,0					_logical			""
BUILD_PROGRAM,0					_build_progs			""
BUILD_EXCLUDE_LAST,0				_logical				""
REFINE_PROGRAM,0				_refine_progs			""
REFINE_CYCLES,0					_positiveint			""
FREE_FRACTION		                	_positivereal			""
REPLACE_MET_MSE				_logical			""

USER_FA_PROGRAM,0					_fa_progs			""
USER_DETECT_PROGRAM,0				_detect_progs			""
USER_DETECT_HIGHRES_CUTOFF,0				_positivereal			""
USER_DETECT_NUM_CYCLES,0				_positiveint			""
USER_DETECT_SPECIAL_POSITIONS,0			_logical			""
USER_DETECT_PATTERSON,0				_logical			""
USER_DETECT_THRESHOLD_SHELX,0				_positivereal			""
USER_DETECT_THRESHOLD_CRUNCH,0				_positivereal			""
USER_PEAK_PROGRAM,0					_peak_progs				""
USER_PEAK_THRESHOLD,0				_positivereal			""
USER_PEAK_CYCLES,0					_positiveint			""
USER_PHASING_PROGRAM,0				_phase_progs			""
USER_PHASING_CYCLES,0				_positiveint			""
USER_HAND_DM_PROGRAM,0					_hand_progs				""
USER_HAND_DM_CYCLES,0					_positiveint			""
USER_HAND_PHASE_COMB_PROGRAM,0			_hand_phase_comb_progs		""
USER_PHASE_COMB_PROGRAM,0				_phase_comb_progs		""
USER_DM_PROGRAM,0					_dm_progs				""
USER_DM_CYCLES,0					_positiveint				""
USER_DM_NCS_PARROT,0					_logical				""
USER_BUILD_CYCLES,0					_positiveint			""
USER_BUILD_CYCLES_MAX,0					_positiveint			""
USER_BUILD_CYCLES_MIN,0					_positiveint			""
USER_BUILD_SKIP_INIT,0					_logical			""
USER_BUILD_PROGRAM,0					_build_progs			""
USER_BUILD_EXCLUDE_LAST,0				_logical				""
USER_REFINE_PROGRAM,0				_refine_progs			""
USER_REFINE_CYCLES,0					_positiveint			""
USER_FREE_FRACTION		                	_positivereal			""
USER_REPLACE_MET_MSE				_logical			""

# defaults not set by crank2 (requiring keyworded input from user) but directly by the gui
BUILD_COMBINED,0				_logical				1
USER_BUILD_COMBINED,0				_logical				1
REFINE_EXCLUDE,0				_logical				1
USER_REFINE_EXCLUDE,0				_logical				1
BUILD_EXCLUDE,0				_logical				1
USER_BUILD_EXCLUDE,0				_logical				1


#     Menus to show information flow between programs          
#                                                              
# These are a series of variable menus that describe the       
# information flow between the programs in the pipeline.       
#                                                              

#
# First, the input columns.  These are what are actually
# displayed on the screen, and allow the user to choose
# the sources of input data for all programs in the pipeline.
#

INPUT_EXPERIMENTAL_COLUMNS,0        		_input_experimental_columns     ""
INPUT_EXPERIMENTAL_COLUMNS_LIST,0   		_list_of_text                   {}
INPUT_EXPERIMENTAL_COLUMNS_ALIAS,0  		_list_of_text                   {}

INPUT_F_COLUMNS,0                   		_input_f_columns                ""
INPUT_F_COLUMNS_LIST,0              		_list_of_text                   {}
INPUT_F_COLUMNS_ALIAS,0             		_list_of_text                   {}

INPUT_I_COLUMNS,0                   		_input_i_columns                ""
INPUT_I_COLUMNS_LIST,0              		_list_of_text                   {}
INPUT_I_COLUMNS_ALIAS,0             		_list_of_text                   {}

INPUT_PHASE_COLUMNS,0               		_input_phase_columns            ""
INPUT_PHASE_COLUMNS_LIST,0          		_list_of_text                   {}
INPUT_PHASE_COLUMNS_ALIAS,0         		_list_of_text                   {}

INPUT_HL_COLUMNS,0                  		_input_hl_columns               ""
INPUT_HL_COLUMNS_LIST,0             		_list_of_text                   {}
INPUT_HL_COLUMNS_ALIAS,0            		_list_of_text                   {}

INPUT_EA_COLUMNS,0                  		_input_ea_columns               ""
INPUT_EA_COLUMNS_LIST,0             		_list_of_text                   {}
INPUT_EA_COLUMNS_ALIAS,0            		_list_of_text                   {}

INPUT_FA_COLUMNS,0                  		_input_fa_columns               ""
INPUT_FA_COLUMNS_LIST,0             		_list_of_text                   {}
INPUT_FA_COLUMNS_ALIAS,0            		_list_of_text                   {}

INPUT_ALPHA_COLUMNS,0               		_input_alpha_columns            ""
INPUT_ALPHA_COLUMNS_LIST,0          		_list_of_text                   {}
INPUT_ALPHA_COLUMNS_ALIAS,0         		_list_of_text                   {}

INPUT_FREER_COLUMNS,0                		_input_freer_columns           	""
INPUT_FREER_COLUMNS_LIST,0           		_list_of_text                  	{}
INPUT_FREER_COLUMNS_ALIAS,0          		_list_of_text                  	{}

INPUT_SUBSTRUCTURE,0               		_input_substructure             ""
INPUT_SUBSTRUCTURE_LIST,0          		_list_of_text                   {}
INPUT_SUBSTRUCTURE_ALIAS,0         		_list_of_text                   {}

INPUT_PDB,0              			_input_pdb                      ""
INPUT_PDB_LIST,0         			_list_of_text                   {}
INPUT_PDB_ALIAS,0        			_list_of_text                   {}

#
# Second, the output columns.  These are not displayed to the
# user, and are instead generated in the procedure crank_run.
#

OUTPUT_EXPERIMENTAL_COLUMNS,0       		_output_experimental_columns 	""
OUTPUT_F_COLUMNS,0                  		_output_f_columns            	""
OUTPUT_I_COLUMNS,0                  		_output_i_columns            	""
OUTPUT_PHASE_COLUMNS,0              		_output_phase_columns        	""
OUTPUT_HL_COLUMNS,0                 		_output_hl_columns           	""
OUTPUT_EA_COLUMNS,0                 		_output_ea_columns           	""
OUTPUT_FA_COLUMNS,0                 		_output_fa_columns           	""
OUTPUT_ALPHA_COLUMNS,0              		_output_alpha_columns        	""
OUTPUT_FREER_COLUMNS,0              		_output_freer_columns        	""
OUTPUT_SUBSTRUCTURE,0               		_output_substructure         	""
OUTPUT_PDB,0                        		_output_pdb                  	""

#
# Third, the defaults.  There is only one default menu per
# step, and it's contents are obtained from crank-defaults.xml.
# The current program determines which menu is displayed
#

DEFAULT_MENU,0                      		_default_menu               	""
DEFAULT_MENU_LIST,0                 		_list_of_text               	{}
DEFAULT_MENU_ALIAS,0                		_list_of_text               	{}

# Generic functions to hold the high and low resolution limits for
# each program step.  We need to store this information because
# if we change the main data structure, the interface will change
# as well.
HIGH_RES_CUTOFF,0               		_positivereal       		""
LOW_RES_CUTOFF,0                		_positivereal       		""

LOW_RES_LIMIT					_positivereal			""
HIGH_RES_LIMIT					_positivereal			""

#   Output Crank run information in a CCP4i database.def file  
#                                                              
# These are a few variables to make it possible for            
# crank_database.com to produce a CCP4i style database.def     
# file.  This file could then be used in a new CCP4i viewer    
# to display the individual steps of a Crank run.             
 
CCP4DB_DATESTR              			_text           		""
CCP4DB_DATE                 			_text           		""
CCP4DB_USER                 			_text           		""
CCP4DB_DATESTR              			_text           		""
CCP4DB_INPUT_FILES,0        			_text           		""
CCP4DB_OUTPUT_FILES,0       			_text           		""
