#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 "2.0.38" 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 ""