# # 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 refmac5 #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" REFINE_TYPE _refmac_refine_type REST RESIDUAL _refmac_residual MLKF MINIMISATION _refmac_minimisation CGMAT EXCLUDE_RESOLUTION _logical 0 EXCLUDE_RESOLUTION_MIN _positivereal "" EXCLUDE_RESOLUTION_MAX _positivereal "" INPUT_PHASE _refmac_input_phase NO PHASE_SCBLUR _real "" PHASE_BBLUR _real "" HKLIN _MTZ_file "" DIR_HKLIN _default_dirs "" HKLOUT _MTZ_file "" DIR_HKLOUT _default_dirs "" TLSIN _tls_file "" DIR_TLSIN _default_dirs "" TLSOUT _tls_file "" DIR_TLSOUT _default_dirs "" XYZIN _pdb_file "" XYZOUT _pdb_file "" DIR_XYZIN _default_dirs "" DIR_XYZOUT _default_dirs "" IFMAPNAMES _logical 0 MAPOUT1 _map_file "" DIR_MAPOUT1 _default_dirs TEMPORARY MAPOUT2 _map_file "" DIR_MAPOUT2 _default_dirs TEMPORARY IF_MAPOUT _logical 0 MAPOUT_FORMAT _map_format MAP_DEFAULT EXTEND_MAP _logical 1 MAP_BORDER _positivereal 5.0 LABIN _text "FP SIGFP" F+ _mtz_label_g "" SIGF+ _mtz_label_l "" F- _mtz_label_g "" SIGF- _mtz_label_l "" NATOMS _positiveint 1 ATOM,0 _text "" ATOM_FP,0 _real "" ATOM_FPP,0 _real "" ATOM,1 _text "" ATOM_FP,1 _real "" ATOM_FPP,1 _real "" WAVELENGTH _positivereal "" REF_SUBOCC _logical 1 IP _mtz_label_j "" SIGIP _mtz_label_sig "" 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 "" 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 "" NCYCLES _positiveint 10 EXTERNAL_NCYCLES _positiveint 5 B_REFINEMENT _logical 1 B_REFINEMENT_MODE _refmac_b_refinement ISOT IFTLS _logical 0 IFFIXTLS _logical 0 TWINREF_TYPE _twinref_type "NO" BLIM _logical 0 BLIM_MIN _positivereal 2.0 BLIM_MAX _positivereal 200.0 EXCLUDE_FREER _logical 1 EXCLUDE_FREER_VALUE _int 0 FREE _mtz_label_freer "" BULK_SOLVENT_SCALING _refmac_scaling SIMPLE SIMPLE_SCALING_RESOLUTION_MIN _resolution "" SIMPLE_SCALING_RESOLUTION_MAX _resolution "" BULK_SCALING_RESOLUTION_MIN _resolution "" BULK_SCALING_RESOLUTION_MAX _resolution "" SCALING_ANISO _logical 1 SCALING_IF_FIXB _logical 0 SCALING_FIXB_BBULK _positivereal "" SCALING_EXPE_SIGMA _logical 1 SCALING_REF_SET _refmac_ref_set working SCALING_APPLY _refmac_scaling_appl observed IF_SOLVENT _logical 1 SOLVENT_VDWPROB _positivereal "" SOLVENT_IONPROB _positivereal "" SOLVENT_RSHRINK _positivereal "" EXPERIMENTAL_WEIGHTING _logical 1 AUTO_WEIGHTING _logical 1 MATRIX_WEIGHT _positivereal "" GRADIENT_WEIGHT _real 1.0 SIGMA_WEIGHT _positivereal 0.5 TLS_NCYCLES _positiveint 10 IFADDU _logical 0 RIGID_NCYCLES _positiveint 20 NDOMAINS _positiveint 0 NGROUPS,0 _positiveint 1 CHAIN1,0 _chain_id "" RES1,0 _res_id "" RES2,0 _res_id "" INITIALISE_RIGID,0 _logical 0 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 # Define first rigid domain INITIALISE_RIGID,0 _logical 0 TRANS_ON,1 _logical 0 TRANS_X,1 _real "" TRANS_Y,1 _real "" TRANS_Z,1 _real "" EULER_ON,1 _logical 0 EULER_ALPHA,1 _real "" EULER_BETA,1 _real "" EULER_GAMMA,1 _real "" EXCLUDE_ATOMS,1 _refmac_rigid_exclude no MAKE_LIBRARY _lib_file "" DIR_MAKE_LIBRARY _default_dirs "" LIBOUT _lib_file "" DIR_LIBOUT _default_dirs "" MAKE_HYDROGEN _refmac_make_hydrogen ALL MAKE_HOUT _logical 0 MAKE_CHECK _refmac_make_check NONE MAKE_PEPTIDE _logical 0 MAKE_CISPEPTIDE _logical 1 MAKE_SSBRIDGE _logical 1 MAKE_SYMMETRY _logical 1 MAKE_NEWLIGAND _logical 0 MAKE_REVIEW _logical 0 MAKE_CONNECTIVITY _refmac_make_link NO MAKE_LINK _refmac_make_link NO MAKE_SUGAR _refmac_make_link YES REVIEW_MAKE_CHECK _refmac_make_check ALL REVIEW_MAKE_PEPTIDE _logical 1 REVIEW_MAKE_CISPEPTIDE _logical 1 REVIEW_MAKE_SSBRIDGE _logical 1 REVIEW_MAKE_SYMMETRY _logical 1 REVIEW_MAKE_CHAIN _logical 1 REVIEW_MAKE_NEWLIGAND _logical 0 REVIEW_MAKE_CONNECTIVITY _refmac_make_link YES REVIEW_MAKE_LINK _refmac_make_link YES REVIEW_MAKE_SUGAR _refmac_make_link YES # Automatic NCS restraints IFAUTONCS _logical 0 AUTONCS_MODE _refmac_autoncs LOCAL # New NCS restraint parameters N_NONX _positiveint 0 N_NONX_CHN_TOTAL,0 _positiveint 0 N_NONX_SPANS_TOTAL,0 _positiveint 0 # RefmacNonX parameters NONX_CHN_SRC,0 _chain_id_menu "" NONX_INIT_SPANS_RES1,0 _residue_id "" NONX_INIT_SPANS_RES2,0 _residue_id "" NONX_INIT_SPANS_CODE,0 _refmac_nonx_code 4 NONX_CHN_TARG,0 _chain_id_menu "" N_NONX_CHN,0 _positiveint 0 N_NONX_SPANS,0 _positiveint 0 # RefmacNonXSpans parameters NONX_SPANS_RES1,0 _residue_id "" NONX_SPANS_RES2,0 _residue_id "" NONX_SPANS_CODE,0 _refmac_nonx_code 4 # RefmacNonXChains parameters NONX_CHN,0 _chain_id_menu "" MONI_LEVEL _refmac_monitor_level MEDIUM MONI_TORSION _positivereal 10.0 MONI_DISTANCE _positivereal 10.0 MONI_ANGLE _positivereal 10.0 MONI_PLANE _positivereal 10.0 MONI_VANDERWAAL _positivereal 3.0 MONI_CHIRAL _positivereal 10.0 MONI_BFACTOR _positivereal 10.0 MONI_BSPHERE _positivereal 10.0 MONI_RBOND _positivereal 10.0 MONI_NCSR _positivereal 10.0 IFSHARP _logical 0 IFBSHARP _logical 0 B_SHARP _real "" IFALSHARP _logical 0 AL_SHARP _real "" # External restraints from Prosmart PROSMART_AVAIL _logical 0 IFPROSMART _logical 0 PROSMART_MODE _prosmart_mode NO USE_PROSMART_KEYFILE _logical 0 PROSMART_KEYFILE _txt_file "" DIR_PROSMART_KEYFILE _default_dirs "" EXT_XYZIN _pdb_file "" DIR_EXT_XYZIN _default_dirs "" # External restraints keywords (Prosmart or general) RESTRAINTFILE _txt_file "" DIR_RESTRAINTFILE _default_dirs "" RESTRAINTFILE_CMD _text "" IFEXTREST_SCALE _logical 1 EXTREST_SCALE _real 10.0 IFEXTREST_USEMAIN _logical 1 IFEXTREST_GMWT _logical 0 EXTREST_GMWT _real 0.15 IFEXTREST_DMAX _logical 1 EXTREST_DMAX _real 4.2 # Secondary structure restraints PROSMART_HELIX _logical 1 PROSMART_STRAND _logical 0 PROSMART_HBOND _logical 1 PROSMART_HBONDHELIX3 _logical 1 PROSMART_HBONDHELIX4 _logical 1 PROSMART_HBONDHELIX5 _logical 1 PROSMART_HBONDSHEET _logical 1 # Begin of definition for External restraints applied to DNA/RNA LIBG_AVAIL _logical 0 IF_LIBG _logical 0 LIBG_MODE _libg_mode AUTOMATED USE_LIBG_DICTFILE _logical LIBG_DICTFILE _txt_file "" DIR_LIBG_DICTFILE _default_dirs "" USE_LIBG_KEYFILE _logical 0 LIBG_KEYFILE _txt_file "" DIR_LIBG_KEYFILE _default_dirs "" # LIBG_EXT_XYZIN _pdb_file "" # DIR_LIBG_EXT_XYZIN _default_dirs "" LIBG_RESTRAINTFILE _txt_file "" DIR_LIBG_RESTRAINTFILE _default_dirs "" LIBG_RESTRAINTFILE_CMD _text "" LIBG_RESTRTYPE _libg_restr_type BP # Base pair IFAUTOBP _logical 0 N_BP _positiveint 0 BP_CHN1,0 _chain_id "" BP_CHN1_RES_FROM,0 _res_id "" BP_CHN1_RES_TO,0 _res_id "" BP_CHN2,0 _chain_id "" BP_CHN2_RES_FROM,0 _res_id "" BP_CHN2_RES_TO,0 _res_id "" LIBG_ALIGN_MODE,0 _libg_align_mode ANTIPARA #Sugar N_SUG _positiveint 0 SUG_CHN,0 _chain_id "" SUG_CHN_RES_FROM,0 _res_id "" SUG_CHN_RES_TO,0 _res_id "" LIBG_SUG_LABEL,0 _libg_sug_label C2ENDO #end of definitions for DNA/RNA restraints IFJELLY _logical 0 JELLY_SIGMA _positivereal 0.02 IFDIST _logical 0 IFANGL _logical 0 IFPLAN _logical 0 IFCHIR _logical 0 IFTMP _logical 0 IFNCSR _logical 0 IFTORS _logical 0 IFVAND _logical 0 IFISO _logical 0 ANGLE_SCALE _positivereal 1.0 WDSKAL _positivereal 1.0 SIGD1 _positivereal "" SIGD2 _positivereal "" SIGD3 _positivereal "" SIGD4 _positivereal "" SIGD5 _positivereal "" WPSKAL _positivereal 1.0 SIGPP _positivereal "" SIGPA _positivereal "" WCSKAL _positivereal 1.0 SIGC _positivereal "" WBSKAL _positivereal 1.0 SIGB1 _positivereal "" SIGB2 _positivereal "" SIGB3 _positivereal "" SIGB4 _positivereal "" IFBFAC_SET _logical 0 BFAC_SET _real 20.0 WSSKAL _positivereal 1.0 SIGSP1 _positivereal "" SIGSP2 _positivereal "" SIGSP3 _positivereal "" SIGSB1 _positivereal "" SIGSB2 _positivereal "" SIGSB3 _positivereal "" WTSKAL _positivereal 1.0 SIGT1 _positivereal "" SIGT2 _positivereal "" SIGT3 _positivereal "" SIGT4 _positivereal "" WVSKAL _positivereal 1.0 WAND_SIGMA_VDW _positivereal "" WAND_SIGMA_HBOND _positivereal "" WAND_SIGMA_METAL _positivereal "" WAND_SIGMA_TORS _positivereal "" WAND_INCR_TORS _real "" WAND_INCR_ADHB _real "" WAND_INCR_AHHB _real "" SPHERICITY _real 5.0 RBOND _real 1.0 RUN_COOT_FW _logical 0 COOT_SIGMA_ADD _real 2.0 COOT_SIGMA_REMOVE _real 1.0 FDISTANCE _logical 1 USE_INCLUDEFILE _logical 0 INCLUDEFILE _any_file "" DIR_INCLUDEFILE _default_dirs "" INCLUDEFILE_CMD _text "" @ [FileJoin [GetEnvPath CCP4I_TOP] tasks harvest.def] # Redundant parameters retained for backwards compatibility WEIGHTING_METHOD _refmac_weighting matrix DAMP _logical 0 DAMP_P _positivereal "" DAMP_B _positivereal "" 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 "" NPARTIALS _positiveint 0 FPART,0 _mtz_label_f "" PHIP,0 _mtz_label_sig "" PARTIAL_SCALE,0 _positivereal 1.0 SPLIT_MODE _refmac_split_mode BINS SPLIT_BINS _positiveint 20 SPLIT_RANGES _positivereal 0.1 SCALING_NCYCYLES _positiveint 10 SCALING_IF_BAVERAGE _logical 0 SCALING_BAVERAGE _positivereal "" SCALING_FIXB_SCBULK _positivereal -0.75 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 IFHOLD _logical 0 PBEL _positivereal 0.3 BDEL _positivereal 3.0 QDEL _positivereal 0.2 MAKE_CHAIN _logical 0 # Internal parameter PREVIOUS_REFINE_TYPE _text "" # Patch for limited length of pname etc. HARVEST_LENSTR _positiveint 10