# # 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 $Id$ # ====================================================================== # detwin.tcl -- # # task interface for truncate program # Also uses rwcontents # # CCP4Interface # # ======================================================================= #------------------------------------------------------------------------- proc detwin_run { arrayname } { #------------------------------------------------------------------------- upvar #0 $arrayname array # Check that a valid operator was selected from the list if { [GetValue $arrayname TWIN_OP_MODE] == "STD" && $array(OPERATOR) == "None" } { WarningMessage "A valid twinning operator is needed to performing detwinning, but one has not been specified. This may be because there are no twinning operators for this spacegroup." return 0 } switch [GetValue $arrayname DETWIN_DATA] \ SCALA { set array(LABIN) "" } SFS { set array(LABIN) "F SIGF" } FPLUS { set array(LABIN) "Fp SIGFp Fm SIGFm" } IMEAN { set array(LABIN) "IMEAN SIGIMEAN" } IPLUS { set array(LABIN) "Ip SIGIp Im SIGIm" } switch [GetValue $arrayname DETWIN_MODE] \ DETWIN { set array(OUTPUT_FILES) HKLOUT } ANALYSIS { set array(OUTPUT_FILES) "" } return 1 } #--------------------------------------------------------------- proc detwin_operator { arrayname } { #--------------------------------------------------------------- upvar #0 $arrayname array set ops None GetTwinData $array(SPACE_GROUP) ops UpdateVariableMenu $arrayname initialise 0 TWIN_OPS_MENU $ops \ TWIN_OPS_ALIAS $ops set array(OPERATOR) [lindex $ops 0] } #--------------------------------------------------------------- proc detwin_setup { typedefVar arrayname } { #--------------------------------------------------------------- upvar #0 $typedefVar typedef set typedef(_detwin_mode) { menu { "Do analysis to determine twinning fraction" "Generate detwinned data" } { ANALYSIS DETWIN } } set typedef(_detwin_data) { menu { "default from Scala" "Fmean" "F+ and F-" "Imean" "I+ and I-" } { SCALA SFS FPLUS IMEAN IPLUS } } set typedef(_twin_op_mode) { menu { "choosing a standard transformation" "entering reflection transformation" } { STD HKL } } set typedef(_twin_operator) { varmenu TWIN_OPS_MENU {} 30 } return 1 } #------------------------------------------------------------------------- proc detwin_task_window { arrayname } { #------------------------------------------------------------------------- upvar #0 $arrayname array SetProgramHelpFile "detwin" if { [CreateTaskWindow $arrayname \ "Detwin - Treat Twinned Data" "Detwin" \ [ list "Required Parameters" ] ] == 0 } return detwin_operator $arrayname OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ message "Chose mode of action" \ widget DETWIN_MODE \ message "Type of data in input MTZ file?" \ label "for input data" \ widget DETWIN_DATA #=FILES================================================================ OpenFolder file CreateInputFileLine line \ "Enter input MTZ file name (HKLIN)" \ "MTZ in" \ HKLIN DIR_HKLIN \ -fileout HKLOUT DIR_HKLOUT "_detwin" \ -setfileparam space_group_name SPACE_GROUP \ -setfileparam resolution_min EXCLUDE_RESOLUTION_MIN \ -setfileparam resolution_max EXCLUDE_RESOLUTION_MAX \ -command "detwin_operator $arrayname" CreateLabinLine line \ "Choose input structure amplitude (F) and sigma (SIGF)" \ HKLIN "F" F { F FP } \ -sigma "SigF" SIGF {} \ -toggle_display DETWIN_DATA open SFS CreateLabinLine line \ "Choose input mean intensity (IMEAN) and sigma (SIGIMEAN)" \ HKLIN "Imean" IMEAN IMEAN\ -sigma "SigImean" SIGIMEAN {} \ -toggle_display DETWIN_DATA open IMEAN OpenSubFrame frame -toggle_display DETWIN_DATA open FPLUS CreateLabinLine line \ "Choose input amplitude (F(+)) and sigma (SIGF(+))" \ HKLIN "F(+)" Fp "F(+)" \ -sigma "SigF(+)" SIGFp {} CreateLabinLine line \ "Choose input amplitude (F(-)) and sigma (SIGF(-))" \ HKLIN "F(-)" Fm "F(-)" \ -sigma "SigF(-)" SIGFm {} CloseSubFrame OpenSubFrame frame -toggle_display DETWIN_DATA open IPLUS CreateLabinLine line \ "Choose input intensity (I(+)) and sigma (SIGI(+))" \ HKLIN "I(+)" Ip "I(+)" \ -sigma "SigI(+)" SIGIp {} CreateLabinLine line \ "Choose input intensity (I(-)) and sigma (SIGI(-))" \ HKLIN "I(-)" Im "I(-)" \ -sigma "SigI(-)" SIGIm {} CloseSubFrame CreateOutputFileLine line \ "Enter name of output MTZ file (HKLOUT)" \ "MTZ out" \ HKLOUT DIR_HKLOUT \ -toggle_display DETWIN_MODE open DETWIN #=PARAMETERS========================================================== OpenFolder 1 open CreateLine line \ message "Define transformation matrix" \ label "Define twinning operator matrix by " \ widget TWIN_OP_MODE CreateLine line \ message "Twinning operator - indices of the reflection related to h,k,l (OPERATOR)" \ label "For space group" \ widget SPACE_GROUP \ -command "detwin_operator $arrayname" \ label "use twinning operator" \ widget OPERATOR \ toggle_display TWIN_OP_MODE open STD CreateLine line \ message "Input twinning operator in form like 'h -k -h/2-l/2' (OPERATOR)" \ help reindex \ label "Use matrix h=" \ widget TWIN_H \ label " k=" \ widget TWIN_K \ label " l=" \ widget TWIN_L \ toggle_display TWIN_OP_MODE open HKL CreateLine line \ message "Apply twinning fraction to detwin the data (TWIN_FRACTION)" \ label "Twin fraction applied to untwin data" \ widget TWIN_FRACTION \ toggle_display DETWIN_MODE open DETWIN CreateLine line \ message "Test data where either Itw1 and Itw2 are greater than Fsig * SigI(SIGMA)" \ label "Sigma cutoff for test" \ widget SIGMA CreateLine line \ message "Exclude reflections below and/or above resolution limit in \ Angstrom (RESOLUTION)" \ help "resolution" \ widget EXCLUDE_RESOLUTION \ -toggleon \ label "Exclude reflections resolution less than" \ widget EXCLUDE_RESOLUTION_MIN \ label "or greater than" \ widget EXCLUDE_RESOLUTION_MAX CreateLine line \ message "Create scatter plot of F1 v F2" \ label "Murray Rust Plot" \ widget PLOT }