# # 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 $Id$ # ====================================================================== # scaleit.tcl -- # # Run scaleit to scale native and derivative data # # CCP4Interface # # ======================================================================= #------------------------------------------------------------------- proc scaleit_setup { typedefVar arrayname } { #------------------------------------------------------------------- upvar #0 $typedefVar typedef set typedef(_scale_mode) { menu { "analysis only" "scale refinement using Scaleit" "scale refinement using Fhscal (Kraut's method)" "Fhscal scale refinement & scaleit analysis" "apply input scale factors" } { ANALYSIS SCALE FHSCAL FHSCALANAL APPLY } } set typedef(_scale_refine_mode) { menu { "scale only" "scale & isotropic Bfactor" "scale & anisotropic Bfactor" } { "SCALE" "ISOTROPIC" "ANISOTROPIC" } } set typedef(_scale_exclude_apply) { varmenu DERIVS_MENU {} 12 } set typedef(_scale_exclude_mode) { menu { "< sigmaF *" "F >" "anomalous SD >" "difference from FP >" } { "SIG" "FMAX" "DMAX" "DIFF" } } return 1 } #---------------------------------------------------------------- proc scaleit_run {arrayname } { #---------------------------------------------------------------- upvar #0 $arrayname array set filename [GetFullFileName0 $arrayname HKLIN] if { $array(ANOMALOUS_DATA) && [file exists $filename] } { set n_pnames 0 if { ![GetParamFromFile MTZ $filename PNAMES pnames] || [set n_pnames [llength $pnames]] < [expr 1 + $array(N_DERIVS)] } { if { [regexp Abort [ChooseOptionDialog "Warning: Scaling Anomalous Data" Warning \ "Correct scaling of anomalous data requires that the data is grouped into datasets in the MTZ file. The file $array(HKLIN) appears to contain $n_pnames datasets. This is less than the number of derivatives plus one (for the native dataset). You might need to Abort and use the 'Edit MTZ Project&Dataset' task in 'Reflection Data Utilities' module." \ [list Continue Abort ] ] ] } { return 0 } } } set array(GRAPH) [expr { $array(ANALYSE_H) || $array(ANALYSE_K) || \ $array(ANALYSE_L) || $array(ANALYSE_MODF) } ] if [regexp ANALYSIS [GetValue $arrayname SCALE_MODE]] { set array(OUTPUT_FILES) "" } else { set array(OUTPUT_FILES) HKLOUT } if { !$array(ANOMALOUS_DATA) } { set array(DISP_DIFF) 0 } return 1 } #---------------------------------------------------------------- proc ScaleitDerivs { arrayname counter } { #---------------------------------------------------------------- upvar #0 $arrayname array UpdateVariableMenu $arrayname append [expr $counter + 2 ] \ DERIVS_MENU [list FPH$counter] CreateLabinLine line \ "Choose derivative amplitude (FPHn) and sigma (SIGFPHn)" \ HKLIN "FPH$counter" FPH [list FPH$counter *[subst $counter]* ] \ -sigma "SigFPH$counter" SIGFPH {} CreateLabinLine line \ "Choose anomalous difference data (DPHn) and sigma (SIGFPHn)" \ HKLIN "DPH$counter " DPH [list DPH$counter *[subst $counter]* ] \ -sigma "SigDPH " SIGDPH {} \ -toggle_display ANOMALOUS_DATA hide 0 OpenSubFrame frame -toggle_display ANOM_DISP_DIFF open 1 CreateLabinLine line \ "Choose derivative amplitude (FPH+n) and sigma (SIGFPH+n)" \ HKLIN "FPH+$counter" FPHp [list FPH+$counter \ *+*[subst $counter]* *[subst $counter]*+*] \ -sigma "SigFPH+$counter" SIGFPHp {} CreateLabinLine line \ "Choose derivative amplitude (FPH-n) and sigma (SIGFPH-n)" \ HKLIN "FPH-$counter" FPHm [list FPH-$counter \ *-*[subst $counter]* *[subst $counter]*-*] \ -sigma "SigFPH-$counter" SIGFPHm {} CloseSubFrame } #-------------------------------------------------------------------------------- proc edit_ScaleitDerivs { arrayname counter } { #-------------------------------------------------------------------------------- # When a deriv is removed need to update variable menu for deriv selection # Beware it is not necessarily the last deriv that was deleted set ll [list "all" "FP" ] if { $counter > 0 } { for { set n 1 } { $n <= $counter } { incr n } { lappend ll "FPH$counter" } } UpdateVariableMenu $arrayname initialise 1 DERIVS_MENU $ll } #---------------------------------------------------------------- proc ScaleitExclude { arrayname counter } { #---------------------------------------------------------------- upvar #0 $arrayname array CreateLine line \ message "Exclude data from scale determination or analysis (EXCLUDE)" \ help exclude \ label "For" \ widget EXCLUDE_APPLY \ label "exclude reflections" \ widget EXCLUDE_MODE \ help exclude_sig \ widget EXCLUDE_SIGMAF \ toggle_display [Indxv EXCLUDE_MODE $counter ] open SIG CreateLine line \ message "Exclude data from scale determination or analysis (EXCLUDE)" \ help exclude \ label "For" \ widget EXCLUDE_APPLY \ label "exclude reflections" \ widget EXCLUDE_MODE \ help exclude_fmax \ widget EXCLUDE_F \ toggle_display [Indxv EXCLUDE_MODE $counter ] open FMAX CreateLine line \ message "Exclude data from scale determination or analysis (EXCLUDE)" \ help exclude \ label "For" \ widget EXCLUDE_APPLY \ label "exclude reflections" \ widget EXCLUDE_MODE \ help exclude_dmax \ widget EXCLUDE_SIGMAD \ toggle_display [Indxv EXCLUDE_MODE $counter ] open DMAX CreateLine line \ message "Exclude data from scale determination or analysis (EXCLUDE)" \ help exclude \ label "For" \ widget EXCLUDE_APPLY \ label "exclude reflections" \ widget EXCLUDE_MODE \ help exclude_diff \ widget EXCLUDE_DIF_FP \ toggle_display [Indxv EXCLUDE_MODE $counter ] open DIFF } #------------------------------------------------------------------ proc ScaleitInputScale { arrayname counter } { #------------------------------------------------------------------ upvar #0 $arrayname array CreateLine line \ message "Input scale factors to apply to on set of data" \ help scale \ label "Scale" \ widget INPUT_SCALE_APPLY \ message "Enter Biso in first column or anistotropic scale factors" \ label "Biso/B11" \ widget INPUT_SCALE_1 \ -width 5 \ label "B22" \ widget INPUT_SCALE_2 \ -width 5 \ label "B33" \ widget INPUT_SCALE_3 \ -width 5 \ label "B12" \ widget INPUT_SCALE_4 \ -width 5 \ label "B13" \ widget INPUT_SCALE_5 \ -width 5 \ label "B23" \ widget INPUT_SCALE_6 \ -width 5 } #----------------------------------------------------------------- proc scaleit_anom_disp_diff { arrayname } { #----------------------------------------------------------------- upvar #0 $arrayname array if { $array(ANOMALOUS_DATA) && $array(DISP_DIFF) } { set array(ANOM_DISP_DIFF) 1 } else { set array(ANOM_DISP_DIFF) 0 } } #----------------------------------------------------------------- proc scaleittestifdnames { arrayname } { #----------------------------------------------------------------- upvar #0 $arrayname array set filename [GetFullFileName0 $arrayname HKLIN] if { [file exists $filename] && [GetParamFromFile MTZ $filename PNAMES pnames] && [llength $pnames] > 0 } { set array(IFDNAMES) 1 set array(IFAUTO) 1 } else { set array(IFDNAMES) 0 set array(IFAUTO) 0 } } #----------------------------------------------------------------- proc scaleit_task_window { arrayname } { #----------------------------------------------------------------- upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "Scaleit - Scale Datasets" "Scale" \ [ list "Parameters" \ "Refinement Parameters" \ "Exclude Reflections" \ "Analysis" \ "Fhscal Scaling Parameters" \ "Input Scaling Factors" ] ] == 0 } return SetProgramHelpFile "scaleit" UpdateVariableMenu $arrayname initialise 1 DERIVS_MENU \ [list "all" "FP" ] scaleit_anom_disp_diff $arrayname #=PROTOCOL============================================================== OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ message "Scale protocol - do refinement or analysis" \ label "Do" \ widget SCALE_MODE CreateLine line \ message "Also apply calculated scales to anomalous differences for derivative data" \ help labin \ widget ANOMALOUS_DATA -command "scaleit_anom_disp_diff $arrayname" \ label "Include anomalous difference data for each derivative" CreateLineTemplate ANOM [list 0.01 0.05 0.5 0.55 ] CreateLine line \ message "Analyse the agreement between the amplitudes for each pair of derivative datasets" \ widget CROSS_COMPARE \ label "Perform cross-comparison of derivative data sets" \ message "Include the anomalous data in the cross-comparison" \ widget DISP_DIFF -command "scaleit_anom_disp_diff $arrayname" \ label "and analyse anomalous differences" \ toggle_display ANOMALOUS_DATA open 1 CreateLine line \ message "Analyse the agreement between the amplitudes for each pair of derivative datasets" \ widget CROSS_COMPARE \ label "Perform cross-comparison of derivative data sets" \ toggle_display ANOMALOUS_DATA open 0 # message "Produce table file containing summary of data analysis" \ # widget TABULATE_ANALYSIS \ # label "Tabulate analysis" \ # toggle_display ANOMALOUS_DATA open 1 #=FILES================================================================ OpenFolder file CreateInputFileLine line \ "Enter input MTZ file name (HKLIN)" \ "MTZ in" \ HKLIN DIR_HKLIN \ -setfileparam space_group_name SPACE_GROUP \ -setfileparam resolution_min EXCLUDE_RESOLUTION_MIN \ -setfileparam resolution_max EXCLUDE_RESOLUTION_MAX \ -fileout HKLOUT DIR_HKLOUT "_scaleit" \ -command "scaleittestifdnames $arrayname" CreateLabinLine line \ "Choose protein amplitude (FP) and sigma (SIGFP)" \ HKLIN "FP " FP {NULL} \ -sigma "SigmaFP " SIGFP {NULL} CreateExtendingFrame N_DERIVS ScaleitDerivs \ "Define MTZ labels for derivative data (FPHn SIGFPHn)" \ "Add Derivative Data" \ [ list FPH SIGFPH \ FPHp SIGFPHp FPHm SIGFPHm \ DPH SIGDPH ] \ -edit edit_ScaleitDerivs CreateOutputFileLine line \ "Enter name for output MTZ file (HKLOUT)" \ "MTZ out" \ HKLOUT DIR_HKLOUT _scaled \ -toggle_display SCALE_MODE hide ANALYSIS #=PARAMETERS========================================================== OpenFolder 1 CreateLine line \ message "Scale over limited resolution range (RESOLUTION)" \ help resolution \ widget EXCLUDE_RESOLUTION -toggleon \ label "Scale over resolution range " \ widget EXCLUDE_RESOLUTION_MIN \ label "to" \ widget EXCLUDE_RESOLUTION_MAX #---------------------------------------------------------------------- # Regular Scaleit input OpenFolder 2 SCALE_MODE open SCALE hide { FHSCAL FHSCALANAL } closed CreateLine line \ help auto \ message "Apply scaling parameters to all structure factor data in same dataset (AUTO)" \ widget IFAUTO \ label "Apply scaling to all structure factor data in same dataset(s) as input data" \ toggle_display IFDNAMES open 1 CreateLine line \ message "Refine the scale factors and isotropic/anomalous Bfactors (REFINE)" \ help refine \ label "Refine" \ widget REFINE_MODE \ label "and " \ help refine_wilson \ widget WILSON_SCALING \ label "apply Wilson scaling" CreateLine line \ message "Weight observations for scale determination by their SDs (WEIGHT)" \ help weight \ widget WEIGHT_BY_SD \ label "Weight observations by their SDs" # CreateLine line \ # label "Convergence Conditions" CreateLine line \ message "Converge after cycles of refinement (CONVERGE NCYC)" \ help converge_ncyc \ widget CONVERGE_NCYC \ label "Converge after" \ widget CONVERGE_NCYC_LIMIT \ label "cycles of refinement" CreateLine line \ message \ "Converge if all absolute shifts < SD of parameter (CONVERGE ABS)" \ help converge_abs \ widget CONVERGE_ABS \ label "Converge if absolute shift <" \ widget CONVERGE_ABS_LIMIT \ label "SDs of parameter" CreateLine line \ message \ "Convergence tolerance (CONVERGE TOL)" \ help converge_tolr \ widget CONVERGE_TOL \ label "Convergence tolerance 10 to power" \ widget CONVERGE_TOL_LIMIT \ #-----------------------------------------------------exclude reflection OpenFolder 3 SCALE_MODE hide FHSCAL closed CreateExtendingFrame NEXCLUDE ScaleitExclude \ "Exclude reflections from some or all datasets" \ "Add Exclusion" \ [list EXCLUDE_MODE \ EXCLUDE_APPLY \ EXCLUDE_SIGMAF \ EXCLUDE_F \ EXCLUDE_SIGMAD \ EXCLUDE_DIF_FP ] #----------------------------------------------------------analysis OpenFolder 4 SCALE_MODE open ANALYSIS hide FHSCAL closed CreateLine line \ message "Analysis v. resolution is always done, also do...(GRAPH)" \ help graph \ label "Include analysis against: " \ widget ANALYSE_H \ label "H " \ widget ANALYSE_K \ label "K " \ widget ANALYSE_L \ label "L " \ widget ANALYSE_MODF \ label "ModF" #----------------------------------------------------------fhscal options SetProgramHelpFile "fhscal" OpenFolder 5 SCALE_MODE open { FHSCAL FHSCALANAL } hide CreateLine line \ message \ "Split into resolution bins, should have >200 reflections per bin (SHELL) " \ help shells \ widget BINS \ label "Split into" \ widget N_BINS \ label "resolution bins" CreateLine line \ message "Use SDs in averaging squares of differences (BIAS)" \ help bias \ widget USE_SDS \ label "Use SIGMAs in averaging squares of differences" CreateLine line \ message "List reflections to output file for analysis (LIST)" \ help list \ widget LIST \ label "List" \ widget LIST_N_REF \ label "reflections to output file" CreateLine line \ message ".. all data is scaled and output (CENTRIC)" \ widget CENTRIC \ label "Use only centric data to compute scale factors" #-------------------------------------------User input of scaling parameters SetProgramHelpFile "scaleit" OpenFolder 6 SCALE_MODE open APPLY hide CreateExtendingFrame N_INPUT_SCALES ScaleitInputScale \ "Input scaling to apply to datasets" \ "Add Scaling Factors" \ [list INPUT_SCALE_APPLY \ INPUT_SCALE_1 \ INPUT_SCALE_2 \ INPUT_SCALE_3 \ INPUT_SCALE_4 \ INPUT_SCALE_5 \ INPUT_SCALE_6 ] }