# # 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 $Id$ # ===================================================================== # prephadata.tcl -- convert Fs to Is for direct methods # ======================================================================= #----------------------------------------------------------------------- proc prephadata_setup { typedefVar arrayname } { #----------------------------------------------------------------------- DefineMenu _prephadata_input [ list "MAD data as F+ F-" \ "MAD data as Dano" \ "SAD data as F+ F-" \ "SAD data as Dano" \ "SIR data" \ "native data" ] \ [ list MADFS MADDS SADFS SADDS SIR NATIVE] DefineMenu _prephadata_output [ list "SHELXS" "SHELXD" "Es (Rantan/Acorn)" "RSPS" ] \ [ list SHELX SHELXD RANTAN CCP4 ] return 1 } #----------------------------------------------------------------------- proc prephadata_run { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array if { [StringSame [GetValue $arrayname REVISE_OUTPUT] CCP4] && [StringSame [GetValue $arrayname REVISE_INPUT ] SADFS SADDS SIR ] } { WarningMessage "No data preparation necessary for SAD or SIR data input to RSPS. Will not run task." return 0 } if { [StringSame [GetValue $arrayname REVISE_INPUT] MADFS MADDS ] } { if { $array(N_WAVELENGTHS) < 2 } { WarningMessage "You need at least two wavelengths for MAD. Will not run task." return 0 } if { $array(USE_REVISE_RESO_CUTOFF) && ![regexp -- "^(\[0-9\]?)(\[\.\])(\[0-9\]*)$" $array(REVISE_RESOLUTION_MAX)]} { WarningMessage "Invalid value for high resolution cutoff. Task run aborted." return 0 } } if { [StringSame [GetValue $arrayname REVISE_OUTPUT] SHELX SHELXD ] } { set array(OUTPUT_FILES) HKLOUT } else { set array(OUTPUT_FILES) MTZOUT } return 1 } #--------------------------------------------------------------------- proc prephadata_anom_labin { arrayname counter } { #--------------------------------------------------------------------- upvar #0 $arrayname array CreateLabinLine line \ "Choose amplitude (FPH+n) and sigma (SIGFPH+n) for wavelength $counter" \ MTZIN "FPH+$counter" FPHp [list FPH+$counter \ "*+*[subst $counter]*" "*[subst $counter]*+*" ] \ -sigma "SigFPH+$counter" SIGFPHp {} CreateLabinLine line \ "Choose amplitude (FPH-n) and sigma (SIGFPH-n) for wavelength $counter" \ MTZIN "FPH-$counter" FPHm [list FPH-$counter \ "*-*[subst $counter]*" "*[subst $counter]*-*" ] \ -sigma "SigFPH-$counter" SIGFPHm {} } #--------------------------------------------------------------------- proc prephadata_dano_labin { arrayname counter } { #--------------------------------------------------------------------- upvar #0 $arrayname array CreateLabinLine line \ "Choose FPH(n) and SIGFPH(n) for wavelength $counter" \ MTZIN "FPH$counter" FPH [list FPH$counter ] \ -sigma "SigFPH$counter" SIGFPH {} CreateLabinLine line \ "Choose DPH(n) and SIGDPH(n) for wavelength $counter" \ MTZIN "DPH$counter" DPH [list DPH$counter ] \ -sigma "SigDPH$counter" SIGDPH {} } # two equivalent procedures prephadata_anom_wavelengths/prephadata_dano_wavelengths # so have two diferent dependent frames for the two case MADFS and MADDS input #--------------------------------------------------------------------- proc prephadata_anom_wavelengths { arrayname counter } { #--------------------------------------------------------------------- upvar #0 $arrayname array CreateLine line \ message "Enter wavelength dataset $counter collected at (Revise WAVE)" \ label "Data set $counter collected at wavelength" \ widget LAMBDA \ label "with estimated F'" \ message"Enter the F' and F'' for this wavelength (WAVE FPR FDP)"\ widget FPRIME -oblig \ label "and F''" \ widget FDPRIME -oblig } #--------------------------------------------------------------------- proc prephadata_dano_wavelengths { arrayname counter } { #--------------------------------------------------------------------- upvar #0 $arrayname array CreateLine line \ message "Enter wavelength dataset $counter collected at (Revise WAVE)" \ label "Data set $counter collected at wavelength" \ widget LAMBDA \ label "with estimated F'" \ message"Enter the F' and F'' for this wavelength (WAVE FPR FDP)"\ widget FPRIME -oblig \ label "and F''" \ widget FDPRIME -oblig } #----------------------------------------------------------------------- proc set_res_max_limit { arrayname limit } { #----------------------------------------------------------------------- upvar #0 $arrayname array if { $array(EXCLUDE_RESOLUTION_MAX) == "" } { return } set array(EXCLUDE_RESOLUTION_MAX) [max $limit \ $array(EXCLUDE_RESOLUTION_MAX)] } #----------------------------------------------------------------------- proc prephadata_update_revise_input { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array if { [StringSame [GetValue $arrayname REVISE_INPUT] SADFS SADDS ] } { set array(ECALC_EXCLUDE_CENTRIC) 1 } else { set array(ECALC_EXCLUDE_CENTRIC) 0 } } #----------------------------------------------------------------------- proc prephadata_task_window { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "Prephadata - Prepare and/or Normalise Reflection Data for Experimental Phasing Programs" "PrepHaData" \ [ list "Anomalous Data" \ "Exclude Data when Calculating Es" \ "Exclude data when converting to Shelx format" ] ] == 0 } return SetProgramHelpFile revise OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ label "Input" \ widget REVISE_INPUT \ -command "prephadata_update_revise_input $arrayname" \ label "and prepare data for" \ widget REVISE_OUTPUT #------------------------------------------------------------------Files OpenFolder file CreateInputFileLine line \ "Enter input MTZ file name (MTZIN)" \ "MTZ in" \ MTZIN DIR_MTZIN \ -fileout MTZOUT DIR_MTZOUT _prephadata \ -fileout HKLOUT DIR_HKLOUT -- \ -setfileparam space_group_name SPACE_GROUP \ -setfileparam resolution_min EXCLUDE_RESOLUTION_MIN \ -setfileparam resolution_max EXCLUDE_RESOLUTION_MAX \ -setfileparam resolution_max REVISE_RESOLUTION_MAX \ -command "set_res_max_limit $arrayname 3.0" CreateLabinLine line \ "Choose native SFs (FP) and optional sigma (SIGFP)" \ MTZIN FP FP {} \ -sigma SIGFP SIGFP {} \ -toggle_display REVISE_INPUT open NATIVE OpenSubFrame frame -toggle_display REVISE_INPUT open SIR CreateLabinLine line \ "Choose native SFs (FP) and optional sigma (SIGP)" \ MTZIN FP FP {} \ -sigma SIGFP SIGFP {} CreateLabinLine line \ "Choose derivative SFs, Dano or Diso (FPH) and optional sigma (SIGPH)" \ MTZIN FPH ECALC_FPH {} \ -sigma SIGFPH ECALC_SIGFPH {} CloseSubFrame OpenSubFrame frame -toggle_display REVISE_INPUT open SADDS CreateLabinLine line \ "Choose anomalous difference Dano (DPH) and optional sigma (SIGDPH)" \ MTZIN DPH ECALC_DPH0 {} \ -sigma SIGDPH ECALC_SIGDPH0 {} CloseSubFrame OpenSubFrame frame -toggle_display REVISE_INPUT open SADFS CreateLabinLine line \ "Choose amplitude (FPH+) and sigma (SIGFPH+)" \ MTZIN "FPH+" FPHp0 [list FPH+ "*+*"] \ -sigma "SigFPH+" SIGFPHp0 {} CreateLabinLine line \ "Choose amplitude (FPH-) and sigma (SIGFPH-)" \ MTZIN "FPH-" FPHm0 [list FPH- "*-*" ] \ -sigma "SigFPH-" SIGFPHm0 {} CloseSubFrame OpenSubFrame frame -toggle_display REVISE_INPUT open MADFS CreateExtendingFrame N_WAVELENGTHS prephadata_anom_labin \ "Add data for another wavelength" \ "Add another wavelength" \ [list FPHp SIGFPHp FPHm SIGFPHm ] \ -dependentframe prephadata_anom_wavelengths CloseSubFrame OpenSubFrame frame -toggle_display REVISE_INPUT open MADDS CreateExtendingFrame N_WAVELENGTHS prephadata_dano_labin \ "Add data for another wavelength" \ "Add another wavelength" \ [list FPH SIGFPH DPH SIGDPH ] \ -dependentframe prephadata_dano_wavelengths CloseSubFrame CreateOutputFileLine line \ "Output MTZ (MTZOUT)" \ "Output MTZ" \ MTZOUT DIR_MTZOUT \ -toggle_display REVISE_OUTPUT hide [list SHELX SHELXD] CreateOutputFileLine line \ "Output Shelx format HKL (HKLOUT)." \ "Output HKL" \ HKLOUT DIR_HKLOUT \ -toggle_display REVISE_OUTPUT open [list SHELX SHELXD] #=PARAMETERS========================================================== OpenFolder 1 REVISE_INPUT open [list MADFS MADDS ] hide OpenSubFrame frame -toggle_display REVISE_INPUT open MADDS CreateExtendingFrame N_WAVELENGTHS prephadata_dano_wavelengths \ "Input estimated wavelength" \ " " [list LAMBDA FPRIME FDPRIME ] \ -noaddline CloseSubFrame OpenSubFrame frame -toggle_display REVISE_INPUT open MADFS CreateExtendingFrame N_WAVELENGTHS prephadata_anom_wavelengths \ "Input estimated wavelength" \ " " [list LAMBDA FPRIME FDPRIME ] \ -noaddline CloseSubFrame CreateLine line \ help reso \ message "Use high resolution cutoff? (RESO)" \ widget USE_REVISE_RESO_CUTOFF \ label "Exclude reflections with resolution higher than" \ message "High resolution cutoff (Angstroms) for Revise (RESO)" \ widget REVISE_RESOLUTION_MAX \ label "A" CreateLine line \ message "Exclude data which has DISO or FPH > Riso (EXCL RISO)" \ label "Exclude data Diso/FPH >" \ help EXCL \ widget RISO \ message "Exclude data which has DANO or FPH > Rano (EXCL RANO)" \ label "or Dano/FPH >" \ widget RANO \ message "Exclude data which has SIGFPH or FPH < sigm (EXCL SIGM)" \ label "or FPH/SIGFPH <" \ widget SIGM #----------------------------------------------exclude data OpenFolder 2 REVISE_OUTPUT close [list RANTAN] hide SetProgramHelpFile ecalc CreateLine line \ message "Exclude data when using Ecalc to calculate Es" \ help exclude \ label "Exclude data with FP <" \ widget ECALC_EXCLUDE_SIGP \ label "*SigFP or FPH <" \ widget ECALC_EXCLUDE_SIGPH \ label "*SigFPH or FP-FPH >" \ widget ECALC_EXCLUDE_DIFF CreateLine line \ message "Exclude data when using Ecalc to calculate Es" \ help exclude \ widget EXCLUDE_RESOLUTION \ label "Exclude reflections with resolution higher than" \ message "High resolution cutoff (Angstroms) for Ecalc (RESO)" \ widget EXCLUDE_RESOLUTION_MAX \ label "A" \ toggle_display REVISE_INPUT open [ list SADFS SADDS SIR ] CreateLine line \ message "Exclude centric data when calculating Es from anomalous differences" \ help exclude \ widget ECALC_EXCLUDE_CENTRIC \ label "Exclude all centric reflections" \ toggle_display REVISE_INPUT open [ list SADFS SADDS ] #--------------------------------------------------mtz2various exclude OpenFolder 3 REVISE_OUTPUT close [list SHELX SHELXD] hide source [SearchPath TOP tasks mtz2var_exclude.tcl ] }