# # 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.tcl -- # # Import a formatted reflection file (eg from Xplor) and create MTZ file # # CCP4Interface # Created Jan97 by Liz Potterton # # ======================================================================= source [SearchPath TOP tasks truncate.tcl] #----------------------------------------------------------------------- proc import_setup { typedefVar arrayname } { #----------------------------------------------------------------------- upvar #0 $typedefVar typedef set typedef(_imprfx_format) { menu {MTZ "ascii MTZ" X-PLOR/CNS SHELX MULTAN TNT mmCIF "user defined" } { MTZ MTZNA4 X-PLOR/CNS SHELX MULTAN TNT CIF USER } } set typedef(_freer_mode) { menu { "keep existing FreeR data" \ "import FreeR data from another MTZ file" \ "generate FreeR data" } { 1 3 2 } } set typedef(_column_name_lines) {int 4 5 20 NOTOBLIG { } } set typedef(_import_truncate_prog) { menu { "Ctruncate" \ "old Truncate" } { CTRUNCATE TRUNCATE } } truncate_setup $typedefVar $arrayname return 1 } #----------------------------------------------------------------------- proc import_run { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array # procedure run before script is written ArrayToList $arrayname NCOL COLUMN_NAME LABOUT ArrayToList $arrayname NCOL COL_TYPE CTYPOUT if { $array(FORTRAN_FORMAT) != "" } { set tt [string trim [string trim $array(FORTRAN_FORMAT) ' ] () ] set array(FORTRAN_FORMAT) "'($tt)'" # Unset the fortran format if the string is empty # This forces f2mtz to use "free" format if { $array(FORTRAN_FORMAT) == "'()'" } { set array(FORTRAN_FORMAT) "" } } set format [GetValue $arrayname FORMAT] if [regexp MTZ$ $format ] { set array(INPUT_FILES) MTZ_INPUT_FILE } elseif [regexp TNT $format ] { set array(INPUT_FILES) TNT_INPUT_FILE } elseif [regexp CIF $format ] { set array(INPUT_FILES) CIF_INPUT_FILE set array(LABIN_FREER) $array(LABIN_FREER_1) } else { set array(INPUT_FILES) HKL_INPUT_FILE } # pname/dname is optional for mmCIF as it should be extracted from # _entry.id and _diffrn.id A more advanced interface would check the file if [regexp CIF $format ] { if { $array(HARVEST_PNAME) != "" && $array(HARVEST_DNAME) != "" } { if { ![SetHarvestParams $arrayname {} -run] } { return 0 } } } else { if { ![SetHarvestParams $arrayname {} -run] } { return 0 } } return 1 } #-------------------------------------------------------------------- proc import_default_format { arrayname } { #-------------------------------------------------------------------- upvar #0 $arrayname array if { $array(FORMAT) == "MTZ" } { set array(FORTRAN_FORMAT) "" } elseif { $array(FORMAT) == "X-PLOR/CNS" } { InitialiseArray [SearchPath TOP tasks import_cns.def ] $arrayname import } elseif { $array(FORMAT) == "SHELX" } { InitialiseArray [SearchPath TOP tasks import_shelx.def ] $arrayname import } elseif { $array(FORMAT) == "MULTAN" } { InitialiseArray [SearchPath TOP tasks import_multan.def ] $arrayname import } elseif { $array(FORMAT) == "TNT" } { InitialiseArray [SearchPath TOP tasks import_tnt.def ] $arrayname import } elseif { $array(FORMAT) == "mmCIF" } { InitialiseArray [SearchPath TOP tasks import_cif.def ] $arrayname import } elseif { $array(FORMAT) == "user defined" } { InitialiseArray [SearchPath TOP tasks import_user.def ] $arrayname import } set w $array(WINDOW) if [winfo exist $w ] { DeleteTaskWindow $w $arrayname import -noexit } UnsetArrayExtras $arrayname RunTask import -array $arrayname if [StringSame $array(FORMAT) SHELX MULTAN USER] { set array(RUN_TRUNCATE) 1 } else { set array(RUN_TRUNCATE) 0 } } #--------------------------------------------------------------------- proc import_update_freermode { arrayname } { #--------------------------------------------------------------------- upvar #0 $arrayname array global typedef if { [llength $array(COLUMNLABELS_LABIN_FREER)] > 1 } { set array(FREER_MODE) [lindex [lindex $typedef(_freer_mode) 1 ] 0] } elseif { [GetValue $arrayname FREER_MODE] == 1 } { set array(FREER_MODE) [lindex [lindex $typedef(_freer_mode) 1 ] 2] } } #--------------------------------------------------------------------- proc import_launch_edit_datasets { arrayname } { #--------------------------------------------------------------------- # User really wants to edit dataset information so close # the current window and launch the appropriate task for them upvar #0 $arrayname array set w $array(WINDOW) if [winfo exist $w ] { DeleteTaskWindow $w $arrayname import -noexit } UnsetArrayExtras $arrayname RunTask edit_dname } #======================================================================= proc ImportColumnsFrame { arrayname i } { #======================================================================= CreateLine line \ message "Data type and label for each input field (CTYPOUT & LABOUT)" \ help labout \ label $i \ widget COL_TYPE \ widget COLUMN_NAME \ format template "COLUMNS" } #=CREATE=WINDOW=AND=SUBWINDOWS=========================================== proc import_task_window { arrayname } { upvar #0 $arrayname array global configure if { [CreateTaskWindow $arrayname \ "Convert to/modify/extend MTZ" "To MTZ" \ [ list "MTZ Project, Crystal & Dataset Names" \ "MTZ Project, Crystal, Dataset Names & Data Harvesting" \ "Cell and Spacegroup to be saved in MTZ file" \ "Detailed specification of import file format" \ "Convert Is to Fs" \ "Creating full/unique dataset" ] ] == 0 } return SetProgramHelpFile "f2mtz" SetHarvestParams $arrayname {} -init #=PROTOCOL============================================================== # Choose format of file to be read OpenFolder protocol CreateTitleLine line TITLE CreateLine format_input \ message "Choose input reflection file format " \ help description \ label "Import reflection file in " \ widget FORMAT \ -command "import_default_format $arrayname" \ label " format and create MTZ file" SetProgramHelpFile cif2mtz CreateLine line \ message "Convert hkl / -h-k-l pairs to F(+) / F(-) columns" \ help anom \ widget ANOMALOUS \ label "Input file contains anomalous data as hkl / -h-k-l pairs" \ toggle_display FORMAT open [list CIF ] SetProgramHelpFile truncate CreateLine line \ message "Convert input intensities to structure factors" \ widget RUN_TRUNCATE \ label "Run" \ widget IMPORT_TRUNCATE_PROG \ label "to convert Is to Fs" \ toggle_display FORMAT open [list SHELX MULTAN USER ] SetProgramHelpFile unique # Uniquiefy is only optional for non-MTZ input OpenSubFrame frame -toggle_display FORMAT hide MTZ CreateLine line \ message "Use uniqueify script to run unique and/or freerflag" \ help description \ widget RUN_UNIQUE \ label "Create full unique set of reflections" \ toggle_display RUN_UNIQUE open { 0 } CreateLine line \ message "Use uniqueify script to run unique and/or freerflag" \ help description \ widget RUN_UNIQUE \ label "Create full unique set of reflections and" \ widget FREER_MODE \ toggle_display RUN_UNIQUE open { 1 } CloseSubFrame # Always run uniqueify for MTZ input CreateLine line \ message "Use uniqueify script to run unique and/or freerflag" \ help description \ label "Create full unique set of reflections and" \ widget FREER_MODE \ toggle_display FORMAT open MTZ # SetProgramHelpFile sftools # CreateLine line \ # message "Run Sftools to check validity of reflection data" \ # help checkhkl \ # widget CHECKHKL \ # label "Run Sftools checkhkl to validate data" #=FILES================================================================ # frame to enter input file name - note there are two different input lines # depending on whether input format is mtz or other - only one line is # displayed at a time SetProgramHelpFile f2mtz OpenFolder file CreateInputFileLine line \ "Enter input MTZ file name " \ "In" \ MTZ_INPUT_FILE DIR_MTZ_INPUT_FILE \ -fileout HKLOUT DIR_HKLOUT _unique \ -setlabin LABIN_FREER { FREE FreeR FreeR_flag FreeRflag} \ -setfileparam resolution_max RESOLUTION_MAX \ -command "import_update_freermode $arrayname" \ -command "UpdateHarvestMTZ $arrayname MTZ_INPUT_FILE" \ -toggle_display FORMAT open MTZ CreateInputFileLine line \ "Enter input reflection file name (HKLIN)" \ "In" \ CIF_INPUT_FILE DIR_CIF_INPUT_FILE \ -fileout HKLOUT DIR_HKLOUT -- \ -toggle_display FORMAT open CIF CreateInputFileLine line \ "Enter input reflection file name (HKLIN)" \ "In" \ HKL_INPUT_FILE DIR_HKL_INPUT_FILE \ -fileout HKLOUT DIR_HKLOUT -- \ -toggle_display FORMAT hide [ list MTZ CIF ] # -setlabinunassigned LABIN_FREER \ CreateInputFileLine line \ "Enter second (FreeR) reflection file name (TNT_INPUT_FILE)" \ "TNT FreeR file" \ TNT_INPUT_FILE DIR_TNT_INPUT_FILE \ -toggle_display FORMAT open TNT CreateInputFileLine line \ "Enter MTZ file name for FreeR data" \ "Import FreeR MTZ" \ IMPORT_FREER_MTZ DIR_IMPORT_FREER_MTZ \ -setlabin IMPORT_FREER_LABIN { FREE FreeR FreeR_flag FreeRflag } \ -toggle_display FREER_MODE open 3 CreateOutputFileLine line \ "Enter output MTZ file name (HKLOUT)" \ "Out" \ HKLOUT DIR_HKLOUT \ -info #=PARAMETERS========================================================== OpenFolder 1 RUN_TRUNCATE open 0 hide OpenSubFrame frame -toggle_display FORMAT hide { MTZ } CreateHarvestLine line -noharvest CloseSubFrame OpenSubFrame frame -toggle_display FORMAT open { MTZ } # Display the project/dataset information but don't allow # the user to edit it CreateLine line \ label "Note that this information cannot be edited here - use Edit MTZ Datasets:" -italic \ button "Launch Edit MTZ Datasets" -command "import_launch_edit_datasets $arrayname" CreateLine line \ label "Crystal" \ varlabel HARVEST_XNAME \ label "belonging to Project" \ varlabel HARVEST_PNAME $line.l2 config -width 20 -background $configure(COLOUR_BACKGROUND) \ -relief groove $line.l4 config -width 20 -background $configure(COLOUR_BACKGROUND) \ -relief groove CreateLine line \ label "Dataset name" \ varlabel HARVEST_DNAME $line.l2 config -width 20 -background $configure(COLOUR_BACKGROUND) \ -relief groove CloseSubFrame OpenFolder 2 RUN_TRUNCATE open 1 hide CreateHarvestLine line -dname #---------------------------------------------------------------------------- OpenFolder 3 FORMAT hide [list MTZ MTZNA4 ] open [list CIF USER] closed CreateLine line \ message "Enter a space group as found in syminfo.lib (SYMMETRY) " \ help symmetry \ label "Space group name or number" \ widget SPACE_GROUP -oblig CreateLine line \ message "Enter cell lengths(Angstrom) and angles(degs) (CELL)" \ help cell \ label "Cell dimensions a" \ widget CELL_1 -width 8 -oblig \ label "b" \ widget CELL_2 -width 8 -oblig \ label "c" \ widget CELL_3 -width 8 -oblig \ label "alpha" \ widget CELL_4 -width 8 -oblig \ label "beta" \ widget CELL_5 -width 8 -oblig \ label "gamma" \ widget CELL_6 -width 8 -oblig #==DETAILED=FORMAT=SPEC================================================ OpenFolder 4 FORMAT hide [list MTZ MTZNA4 CIF] open [list USER X-PLOR/CNS] closed CreateLine line \ " " \ label "X-plor/CNS formats are variable. Please check this line:" -italic \ toggle_display FORMAT open X-PLOR/CNS CreateLine line \ message "Fortran specification of the format (FORMAT)" \ help format \ label "Fortran format" \ widget FORTRAN_FORMAT -width 25 -expand \ message "Skip number of lines at top of file (SKIP)" \ help skip \ label " Skip first" \ widget SKIPLINE -width 5 \ label "lines" CreateLine line \ " " \ label "Data type and label for input fields" #Frame to enter the column types CreateLineTemplate "COLUMNS" {0.0 0.04 0.5 } CreateExtendingFrame NCOL ImportColumnsFrame \ "Add/remove line to define extra column in MTZ file " \ "Add column label" \ [ list COL_TYPE \ COLUMN_NAME ] #--------------------------------------------------------truncate OpenFolder 5 RUN_TRUNCATE open 1 hide SetProgramHelpFile "truncate" CreateLine line \ message "Labels should correspond to those defined in format above (LABIN)" \ help "labin" \ label "Input labels Imean" \ widget IMEANIN \ -width 20 \ label "SigmaI" \ widget SIGIMEANIN \ -width 20 truncate_define_contents $arrayname truncate_options $arrayname #=UNIQUE/FULL=DATASET==================================================== OpenFolder 6 RUN_UNIQUE open [list 1 ] hide SetProgramHelpFile "freerflag" OpenSubFrame frame -toggle_display FREER_MODE open 1 CreateLine line \ message "Use existing FreeR" \ label "FreeR column label" \ widget LABIN_FREER \ toggle_display FORMAT open MTZ CreateLine line \ message "New FreeR column name" \ label "FreeR column label" \ widget LABIN_FREER_1 \ toggle_display FORMAT hide MTZ CloseSubFrame CreateLine line \ message "Use FreeR from an existing MTZ file" \ help description \ label "Copy FreeR data from " \ widget IMPORT_FREER_LABIN \ toggle_display FREER_MODE open 3 CreateLine line \ message " ..or choose fraction of reflections for freeR" \ help freerfrac \ label "Set FreeR for fraction of reflections" \ widget FREER_FRACTION \ toggle_display FREER_MODE open 2 SetProgramHelpFile cad CreateLine line \ message "Include systematic absences in the full unique dataset?" \ help sysab \ widget INCL_SYS_ABS \ label "Include systematic absences" CreateLine line \ message "Extend resolution" \ help resolution \ widget EXTEND_RESOLUTION \ -toggleon \ label "Extend resolution to" \ widget RESOLUTION_MAX }