# # 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 $Id$ # ====================================================================== # import_scaled.tcl -- # # Import a formatted reflection file from either SCALEPACK or D*TREK and # create an MTZ file with intensities - convert to SFs using truncate # # CCP4Interface # Aug01 by Peter Briggs, from the scalepack2mtz and dtrek2mtz # tasks originally created by Liz Potterton. # # ======================================================================= source [SearchPath TOP tasks truncate.tcl] #------------------------------------------------------------------------ proc import_scaled_setup { typedefname arrayname } { #------------------------------------------------------------------------ upvar #0 $typedefname typedef truncate_setup $typedefname $arrayname DefineMenu _import_format [list "Scalepack (DENZO)" "d*trek"] \ [ list SCALEPACK DTREK ] DefineMenu _import_truncate_id [list "dataset name" \ "user defined identifier" ] \ [ list DATASET USER ] DefineMenu _import_truncate_prog [list "Ctruncate" "old Truncate"] \ [ list CTRUNCATE TRUNCATE ] return 1 } #--------------------------------------------------------------------- proc import_scaled_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" } } # Set the list of INPUT_FILES to the correct logical name for the # type of data being imported if { [GetValue $arrayname IMPORT_FORMAT] == "SCALEPACK" } { set array(INPUT_FILES) HKLIN_SCA } elseif { [GetValue arrayname IMPORT_FORMAT] == "DTREK" } { set array(INPUT_FILES) HKLIN_REF } # suppress warnings about harvest dataset names for now because ctruncate doesn't do harvesting #if { ![SetHarvestParams $arrayname {} -run] } { return 0 } # Sort out the label identifiers for truncate if { $array(RUN_TRUNCATE) } { import_scaled_truncate_labout $arrayname } else { # if you don't run Truncate then have to output Is set array(OUTPUT_I) 1 } return 1 } #---------------------------------------------------------------------- proc read_dtrek_header { arrayname } { #---------------------------------------------------------------------- upvar #0 $arrayname array # Try and read in the cell and spacegroup from header information in # the dtrek file # Read the first 10 lines - then stop set filename [GetFullFileName0 $arrayname HKLIN_REF] if { [file exists $filename] && [OpenFile $filename f r ] } { for { set n 0 } { $n < 10 } { incr n } { catch "gets $f line" set words [ split $line = ] if { [ llength $words ] == 2 } { set first_word [ lindex $words 0 ] if { [string match CRYSTAL_SPACEGROUP $first_word ] } { set space_group [string trim [lindex $words 1] ";" ] } elseif { [string match CRYSTAL_UNIT_CELL $first_word ] } { set cell_params [split [lindex $words 1] ] if { [llength $cell_params] == 6 } { set ii -1 for { set i 1 } { $i <= 6 } { incr i } { incr ii set cell($i) [string trim [lindex $cell_params $ii] ";"] } } } } } CloseFile $f } # Check if the information read in makes sense set cell_ok 1 for { set i 1 } { $i <= 6 } { incr i } { # Cell parameters must be positive and non-zero if { ![info exists cell($i) ] } { set cell_ok 0 } elseif { $cell($i) <= 0 } { set cell_ok 0 } } # Only load the parameters if the cell checks out as reasonable if { $cell_ok } { for { set i 1 } { $i <= 6 } { incr i } { set array(CELL_$i) $cell($i) } if { [info exists space_group] } { set array(SPACE_GROUP) $space_group } } } #---------------------------------------------------------------------- proc read_scalepack_header { arrayname } { #---------------------------------------------------------------------- upvar #0 $arrayname array # Read the 3rd line of the scalepack file to get cell and perhaps spacegroup # Warning: maybe there is no header? # We need to check that the extracted values are sensible set filename [GetFullFileName0 $arrayname HKLIN_SCA] 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 } { $i <= 6 } { incr i } { incr ii set cell($i) [lindex $line $ii] } if { [llength $line] >= 7 } { set space_group [lindex $line 6] } } ## 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 } # Check if the information read in makes sense set cell_ok 1 for { set i 1 } { $i <= 6 } { incr i } { # Cell parameters must be positive and non-zero if { ![info exists cell($i) ] } { set cell_ok 0 } elseif { $cell($i) <= 0 } { set cell_ok 0 } } # Only load the parameters if the cell checks out as reasonable if { $cell_ok } { for { set i 1 } { $i <= 6 } { incr i } { set array(CELL_$i) $cell($i) } # cannot handle r3, so switch to h3 regsub -nocase {r3} $space_group h3 space_group if { [info exists space_group] } { set array(SPACE_GROUP) $space_group } } } #------------------------------------------------------------------------- proc import_scaled_truncate_labout { arrayname } { #------------------------------------------------------------------------- upvar #0 $arrayname array # Reset the identifier depending on whether the user wants # dataset name or user-defined labels if { [GetValue $arrayname COLUMN_ID_TYPE] == "DATASET" } { set array(LABOUT_LABEL) $array(HARVEST_DNAME) } else { set array(LABOUT_LABEL) $array(USER_LABOUT_LABEL) } # Update the labels truncate_labout $arrayname } #------------------------------------------------------------------------- proc import_scaled_task_window { arrayname } { #------------------------------------------------------------------------- upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "ImportScaled - Import Scaled Data from Denzo or d*trek" "Scalepack/dtrek" \ [ list "MTZ Project, Crystal, Dataset Names & Data Harvesting" \ "MTZ Project, Crystal & 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 "Has the data come from DENZO/Scalepack or from d*trek?" \ label "Convert scaled data output from" \ widget IMPORT_FORMAT \ label "into MTZ format" CreateLine line \ message "Does the file contain anomalous data? (ANOMALOUS)" \ widget ANOMALOUS \ label "Use anomalous data" SetProgramHelpFile truncate CreateLine line \ message "Convert input intensities to structure factors" \ widget RUN_TRUNCATE \ label "Run" \ widget IMPORT_TRUNCATE_PROG \ label "to convert intensities to structure factors" CreateLine line \ message "Keep the input intensities in the output MTZ file" \ widget OUTPUT_I \ label "Keep the input intensities in the output MTZ file" \ toggle_display RUN_TRUNCATE open 1 UniqueifyFrame1 $arrayname #=FILES================================================================ OpenFolder file CreateInputFileLine line \ "Enter input reflection file name for Scalepack data (HKLIN)" \ "In" \ HKLIN_SCA DIR_HKLIN_SCA \ -fileout HKLOUT DIR_HKLOUT -- \ -command "read_scalepack_header $arrayname" \ -toggle_display IMPORT_FORMAT open [list SCALEPACK] CreateInputFileLine line \ "Enter input reflection file name for d*trek data (HKLIN)" \ "In" \ HKLIN_REF DIR_HKLIN_REF \ -fileout HKLOUT DIR_HKLOUT -- \ -command "read_dtrek_header $arrayname" \ -toggle_display IMPORT_FORMAT open [list DTREK] UniqueifyFrame2 CreateOutputFileLine line \ "Enter output MTZ file name (HKLOUT)" \ "Out" \ HKLOUT DIR_HKLOUT \ -info OpenSubFrame frame -toggle_display RUN_TRUNCATE open 1 CreateLine line \ message "Decide how to identify columns from different datasets" \ label "Use" \ widget COLUMN_ID_TYPE \ -command "import_scaled_truncate_labout $arrayname"\ label "as identifier to append to column labels" CreateLine line \ message "Enter an identifier for this data set to append to column labels" \ label "Identifier to append to column labels" \ widget USER_LABOUT_LABEL \ -command "import_scaled_truncate_labout $arrayname" \ toggle_display COLUMN_ID_TYPE hide DATASET CloseSubFrame #=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 CreateLine line \ message "Enter wavelength (Angstroms) that this dataset was collected at (WAVE)" \ help wave \ label "Data collected at wavelength" \ widget LAMBDA -oblig \ label "Angstroms" 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 IMPORT_TRUNCATE_PROG hide [list CTRUNCATE] closed truncate_options $arrayname # Initialise labels import_scaled_truncate_labout $arrayname }