# # 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 $Id$ # ====================================================================== # scalepack2mtz.tcl -- # # Import a formatted reflection file from DENZO and create multirecord # MTZ file - convert to SFs using truncate # # CCP4Interface # Created Oct97 by Liz Potterton # # ======================================================================= source [SearchPath TOP tasks truncate.tcl] #------------------------------------------------------------------------ proc scalepack2mtz_setup { typedefname arrayname } { #------------------------------------------------------------------------ upvar #0 $typedefname typedef truncate_setup $typedefname $arrayname return 1 } #--------------------------------------------------------------------- proc scalepack2mtz_run { arrayname } { #--------------------------------------------------------------------- upvar #0 $arrayname array if { $array(USE_LABOUT) } { if { $array(ANOMALOUS) } { set array(LABOUT) "IMEAN SIGIMEAN Ip SIGIp Im SIGIm F SIGF DANO SIGDANO Fp SIGFp Fm SIGFm ISYM" } else { set array(LABOUT) "IMEAN SIGIMEAN F SIGF" } } if { ![SetHarvestParams $arrayname {} -run] } { return 0 } return 1 } #---------------------------------------------------------------------- proc read_scalepack_header { arrayname } { #---------------------------------------------------------------------- upvar #0 $arrayname array # Read the 3rd line of the scalepack file to get cell and perhaps spacegroup set filename [GetFullFileName0 $arrayname HKLIN] if { [file exists $filename] && [OpenFile $filename f r ] } { for { set n 1 } { $n <= 3 } { incr n } { catch "gets $f line" } if { [llength $line] >= 6 } { set ii -1; for { set i 1 } { $i <= 6 } { incr i } { incr ii set array(CELL_$i) [lindex $line $ii] # SimulateReturn $arrayname CELL_$i } if { [llength $line] >= 7 } { set array(SPACE_GROUP) [lindex $line 6] # SimulateReturn $arrayname SPACE_GROUP } } ## read a line of reflection data - does it include anomalous (4 data columns) ## or no anomalous (2 data columns) # for { set n 1 } { $n <= 3 } { incr n } { catch "gets $f line" } # if { [llength $line] == 5 } { # set array(ANOMALOUS) 0 # } elseif { [llength $line] == 7 } { # set array(ANOMALOUS) 1 # } CloseFile $f } } #======================================================================= proc ScalepackRejects { arrayname i } { #======================================================================= CreateLine line \ message "Enter h,k,l for reflection to be excluded from output file" \ help "reject" \ label "Reject reflection(s) h" \ widget REJECT1_H \ label "k" \ widget REJECT1_K \ label "l" \ widget REJECT1_L \ label " and h" \ widget REJECT2_H \ label "k" \ widget REJECT2_K \ label "l" \ widget REJECT2_L } #------------------------------------------------------------------------- proc scalepack2mtz_task_window { arrayname } { #------------------------------------------------------------------------- upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "Scalepack2MTZ - Import Scaled Denzo Data" "Scalepack" \ [ list "MTZ Project & Dataset Names & Data Harvesting" \ "MTZ Project & Dataset Names" \ "Extra Information for MTZ File" \ "Edit or Transform Input Data" \ "Log File Output" \ "Conversion to SFs Parameters" ] ] == 0 } return SetHarvestParams $arrayname {} -init #=PROTOCOL============================================================== # Choose format of file to be read OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ message "Use anomalous data (ANOMALOUS)" \ widget ANOMALOUS \ label "Use anomalous data" \ toggle_display FORMAT open SCALEPACK SetProgramHelpFile truncate CreateLine line \ message "Convert input intensities to structure factors" \ widget RUN_TRUNCATE \ label "Run Truncate to convert intensities to structure factors" UniqueifyFrame1 $arrayname #=FILES================================================================ CreateInputFileLine line \ "Enter input reflection file name (HKLIN)" \ "In" \ HKLIN DIR_HKLIN \ -fileout HKLOUT DIR_HKLOUT -- \ -command "read_scalepack_header $arrayname" UniqueifyFrame2 CreateOutputFileLine line \ "Enter output MTZ file name (HKLOUT)" \ "Out" \ HKLOUT DIR_HKLOUT \ -info CreateLine line \ message "Enter an identifier for this data set to append to column labels" \ label "Identifier to append to column labels" \ widget LABOUT_LABEL \ -command "truncate_labout $arrayname" #=PARAMETERS========================================================== OpenFolder 1 RUN_TRUNCATE open 1 hide CreateHarvestLine line -dname OpenFolder 2 RUN_TRUNCATE open 0 hide CreateHarvestLine line -noharv #------------------------------------------------------------------------ OpenFolder 3 CreateLine line \ message "Enter the number code for the space group (SYMMETRY) " \ help "symmetry" \ label "Space group" \ widget SPACE_GROUP -oblig CreateLine line \ message "Enter cell lengths(Angstrom) and angles(degs) (CELL)" \ help "cell" \ label "Cell dimensions " \ widget CELL_1 -oblig \ widget CELL_2 -oblig \ widget CELL_3 -oblig \ widget CELL_4 -oblig \ widget CELL_5 -oblig \ widget CELL_6 -oblig SetProgramHelpFile truncate CreateLine line \ label "Estimated number of residues in the asymmetric unit" \ help NRESIDUES \ widget CONTENTS_NRES -oblig \ toggle_display RUN_TRUNCATE open 1 #==EDIT / TRANSFORM INPUT DATA========================================= OpenFolder 4 closed SetProgramHelpFile scalepack2mtz CreateLine line \ message "Set resolution limits on data (RESOLUTION)" \ help "resolution" \ widget RESOLUTION_RANGE \ -toggleon \ label "Set resolution limits to min" \ widget RESOLUTION_MIN \ label "and max" \ widget RESOLUTION_MAX CreateLine line \ message "Multiply input intensities by scaling factor (SCALE)" \ label "Scale input intensities by" \ widget SCALE # CreateLine line \ # message "Reindex the reflections by applying transformation (REINDEX)" \ # widget REINDEX \ # label "Reindex transformation: h=" \ # widget REINDEX_H \ # label " k=" \ # widget REINDEX_K \ # label " l=" \ # widget REINDEX_L CreateLine line \ label "Exclude the following reflections from the output file" -italic CreateExtendingFrame N_REJECTS HklRejects \ "Define reflections to be excluded from file" \ "Add Reject" \ [list REJECT1_H \ REJECT1_K \ REJECT1_L \ REJECT2_H \ REJECT2_K \ REJECT2_L ] OpenFolder 5 closed CreateLine line \ message "Write diagnostic to log file (MONITOR)" \ help "monitor" \ widget USE_MONITOR \ -toggleon \ label "Monitor every" \ widget MONITOR \ label "reflection" #-------------------------------------------------------------------truncate OpenFolder 6 closed truncate_options $arrayname }