# # 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 $Id$ # ====================================================================== # ncsref.tcl -- # # Run Mapmask to generate mask for one ncs unit and then use # DM to get ncs phases # # CCP4Interface # # ======================================================================= #-------------------------------------------------------------------- proc ncsref_setup { typedefVar arrayname } { #-------------------------------------------------------------------- upvar #0 $typedefVar typedef set typedef(_refmac_nonx_code) { menu { "tight" \ "tight main chain & medium side chain" \ "tight main chain & loose side chain" \ "medium" \ "medium main chain & loose side chain" \ "loose" } { 1 2 3 4 5 6 } } return 1 } #-------------------------------------------------------------------- proc ncsref_run { arrayname } { #-------------------------------------------------------------------- upvar #0 $arrayname array # Check that the solvent fraction is valid set solvent_warning 0 if { [string trim $array(SOLVENT_FRAC)] == "" } { set solvent_warning 1 } elseif { ![string is double $array(SOLVENT_FRAC)] } { set solvent_warning 1 } elseif { $array(SOLVENT_FRAC) < 0.0 || \ $array(SOLVENT_FRAC) > 1.0 } { set solvent_warning 1 } if { $solvent_warning } { WarningMessage "You need to enter a valid value for the solvent fraction (in the \"Required Parameters\" folder). This should be a decimal fraction between 0.0 (indicating all protein) and 1.0 (all solvent)." return 0 } return 1 } #--------------------------------------------------------------------- proc NcsrefUnits { arrayname counter } { #--------------------------------------------------------------------- upvar #0 $arrayname array SetProgramHelpFile lsqkab CreateLine line \ message "Define chain for NCS unit" \ label "NCS unit $counter is chain" \ help match \ widget CHAIN \ label "residue range" \ widget CHAIN_RES_1 \ label to \ widget CHAIN_RES_2 } #------------------------------------------------------------------------ proc RefmacNonX { arrayname c1 } { #------------------------------------------------------------------------ CreateExtendingFrame N_NONX_CHN RefmacNonXChain \ "Specify chains restrained by non-crystallographic symmetry" \ "Add chain" \ [list NONX_CHN ] \ -counter $c1 CreateExtendingFrame N_NONX_SPANS RefmacNonXSpans \ "Specify range of residues restrained by non-crystallographic symmetry" \ "Add residue range" \ [list NONX_SPANS_RES1 \ NONX_SPANS_RES2 \ NONX_SPANS_CODE ] \ -counter $c1 } #------------------------------------------------------------------------ proc RefmacNonXChain { arrayname c1 c2 } { #------------------------------------------------------------------------ if { $c1 == 1 } { CreateLine line \ label "Restrain together chain" \ widget NONX_CHN } else { CreateLine line \ label "and" \ widget NONX_CHN } } #------------------------------------------------------------------------ proc RefmacNonXSpans { arrayname c1 c2 } { #------------------------------------------------------------------------ CreateLine line \ label "Restrain residue range" \ widget NONX_SPANS_RES1 \ label "to" \ widget NONX_SPANS_RES2 \ label "with" \ widget NONX_SPANS_CODE \ label "restraints" } #------------------------------------------------------------------- proc NcsrefReadPdb { arrayname } { #------------------------------------------------------------------- upvar #0 $arrayname array source [SearchPath TOP utils pdb_utils.tcl] if { [PdbGetChains [GetFullFileName0 $arrayname XYZIN] chains chain_res] && [llength $chains] > 0 } { set increment [expr [llength $chains] - $array(NCHAINS) ] update_extendingframe NcsrefUnits 0 $arrayname NCHAINS \ $array(NCHAINS) $increment 1 for { set n 1 } { $n <= $array(NCHAINS) } { incr n } { set array(CHAIN,$n) [lindex $chains [expr $n -1] ] set array(CHAIN_RES_1,$n) [lindex [lindex $chain_res [expr $n -1] ] 0] set array(CHAIN_RES_2,$n) [lindex [lindex $chain_res [expr $n -1] ] 1] } } } #-------------------------------------------------------------------- proc ncsref_task_window {arrayname} { #-------------------------------------------------------------------- upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "NCSref - NCS Phased Refinement" NCSRef \ [list "NCS Units" \ "Required Parameters" \ "Detailed Parameters" ] ] == 0 } return SetDefaultMapFormat $arrayname MAPOUT_FORMAT SetProgramHelpFile refmac #=PROTOCOL============================================================== OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ message "By default initial phases calculated by Refmac" \ widget INIT_PHASE \ label "Input initial phases" CreateLine line \ message "Generate weighted mFo-DFcalc and 2mFo-DFcalc maps & averaged maps" \ widget IF_MAPOUT \ -toggleon \ label "Generate weighted difference maps files in" \ widget MAPOUT_FORMAT \ label "format" #=FILES================================================================ OpenFolder file CreateInputFileLine line \ "Enter input coordinate file (XYZIN)" \ "Coords in" \ XYZIN DIR_XYZIN \ -command "NcsrefReadPdb $arrayname" \ -fileout XYZOUT DIR_XYZOUT "_ncsref" CreateOutputFileLine line \ "Enter name of output coordinate file (XYZOUT)" \ "Coords out" \ XYZOUT DIR_XYZOUT CreateInputFileLine line \ "Enter input MTZ file name (HKLIN)" \ "MTZ in" \ HKLIN DIR_HKLIN \ -setlabin FREE [list FREE FreeR FreeR_flag] \ -fileout HKLOUT DIR_HKLOUT "_ncsref" \ -fileout MASKOUT DIR_MASKOUT "_ncsref" CreateLabinLine line \ "Choose amplitude (FP) and essential sigma (SIGFP)" \ HKLIN "FP" FP {} \ -sigma "SIGFP" SIGFP {} CreateLabinLine line \ "Choose phase (PHIO) and essential weighting factor (FOMO)" \ HKLIN "PHIO" PHIO {} \ -sigma "Weight" FOMO {} \ -toggle_display INIT_PHASE open 1 CreateLabinLine line \ "Choose COMPULSORY Free R column (FREE)" \ HKLIN FreeR FREE {} CreateOutputFileLine line \ "Enter name of output MTZ file (HKLOUT)" \ "MTZ out" \ HKLOUT DIR_HKLOUT CreateOutputFileLine line \ "Enter name of output mask file (MASKOUT)" \ "Mask out" \ MASKOUT DIR_MASKOUT #=PARAMETERS========================================================== OpenFolder 1 # CreateToggleFrame N_NONX RefmacNonX \ # "Open another non-xtallographic symmetry restraint" \ # "Non-xtallographic symmetry restraint" \ # "Add non-X restraint" \ # [list N_NONX_CHN \ # N_NONX_SPANS ] \ # -child RefmacNonXChain \ # -child RefmacNonXSpans CreateExtendingFrame NCHAINS NcsrefUnits \ "Add/remove line to define NCS unit" \ "Add NCS unit" \ [ list CHAIN \ CHAIN_RES_1 \ CHAIN_RES_2 ] #------------------------------------------------------------------------- OpenFolder 2 SetProgramHelpFile refmac CreateLine line \ message "Number of cycles of refinement (NCYC) for each Refmac run" \ help refi_ncyc \ widget NCYCLES \ -width 3 \ label "cycles of refinement in each Refmac run and" \ message "Number of cycles of running Refmac & DM" \ widget EXTERNAL_NCYCLES \ -width 3 \ label "cycle(s) of external refinement" \ SetProgramHelpFile dm CreateLine line \ message "Fraction of unit cell which is solvent (SOLC) as a fraction between 0.0 and 1.0" \ help solc \ label "Fraction solvent content" \ widget SOLVENT_FRAC -oblig #-------------------------------------------------------------------------detailed parameters OpenFolder 3 closed SetProgramHelpFile ncsmask CreateLine line \ message "Atom radius used in generating mask (RADIUS)" \ label "Atom radius used in generating mask" \ widget RADIUS SetProgramHelpFile refmac CreateLine line \ message "Blurring factors for input phases (REFI PHASE SCBLUR BBLUR)" \ label "Blurring factors for input phase FOM SC" \ help refi_phas_scbl \ widget PHASE_SCBLUR \ label "B" \ widget PHASE_BBLUR CreateLine line \ message "For structures with non-robust Wilson plot fix (SCALE FIXB)" \ help "scal_lssc_fixb" \ widget SCALING_IF_FIXB \ -toggleon \ label "Fix overall scales and Bvalues for bulk to" \ widget SCALING_FIXB_BBULK \ label "and solvent/protein density ratio" \ widget SCALING_FIXB_SCBULK }