# # 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]