# # 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 $Id$ # ====================================================================== # fft.tcl -- # # Run fft to generate a map (does not cover Pattersons) # # CCP4Interface # # ====================================================================== #----------------------------------------------------------------------- proc fft_setup { typedefVar arrayname } { #----------------------------------------------------------------------- upvar #0 $typedefVar typedef DefineMenu _fft_whichhand [list "original hand" "opposite hand"] \ [list "" "HAND 2"] return 1 } #----------------------------------------------------------------------- proc fft_run { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array if { [regexp MAP [GetValue $arrayname FFTPROGRAM ]] && [ regexp INPUT [GetValue $arrayname MAP_LIMITS_MODE]] && [regexp CCP4 [GetValue $arrayname FFT_MAP_FORMAT ]] && !$array(IFPEAKSEARCH) && !$array(RUN_NPO) } { WarningMessage "This setup will not do anything!!" return 0 } if [StringSame $array(LABIN) anomalous] { set array(SIG1) $array(SIGDANO) } else { set array(SIG1) $array(SIGF1) } if { [StringSame $array(LABIN) simple anomalous] } { # Set flag to indicate whether or not F2 label will be used for FFT set array(USE_F2) 0 } else { set array(USE_F2) 1 } if [regexp MAP [GetValue $arrayname FFTPROGRAM ]] { set array(INPUT_FILES) MAPIN } else { set array(INPUT_FILES) HKLIN } if [StringSame [GetValue $arrayname MAP_LIMITS_MODE] PDB ] { append array(INPUT_FILES) " " EXTEND_XYZIN } if { $array(IFMAPOUT) } { switch [GetValue $arrayname FFT_MAP_FORMAT ] \ CCP4 { set array(OUTPUT_FILES) MAPOUT } O { set array(OUTPUT_FILES) O_MAPOUT } QUANTA { set array(OUTPUT_FILES) Q_MAPOUT } } else { set array(OUTPUT_FILES) "" } if { $array(RUN_NPO) && \ [regexp FILE [GetValue $arrayname COORDS_MODE]] } { append array(INPUT_FILES) " XYZ_FILE" } if { $array(IFPEAKSEARCH) } { append array(OUTPUT_FILES) " XYZPEAKS" } if { $array(EXCLUDE_BYSIGMA) } { if { ![regexp "PATTERSONI" $array(PATTERSON_MODE)] } { if { [string trim $array(EXCLUDE_BYSIGMA_1)] == "" && [string trim $array(EXCLUDE_BYSIGMA_2)] == "" } { WarningMessage "No sigma levels have been given for excluding F less than n* sigmaF. Please correct and rerun." return 0 } } } return 1 } #----------------------------------------------------------------------- proc fft_extent { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array set mode [GetValue $arrayname MAP_LIMITS_MODE] if { [ GetValue $arrayname FFTPROGRAM ] == "MAP" } { UpdateVariableMenu $arrayname initialise 0 MAP_LIMITS_MENU \ [list "as input map" \ "all atoms in PDB file" \ "extent defined by user" ] \ MAP_LIMITS_ALIAS [list INPUT PDB USER ] if { $mode == "INPUT" } { set array(MAP_LIMITS_MODE) "as input map" } } else { UpdateVariableMenu $arrayname initialise 0 MAP_LIMITS_MENU \ [list "asymmetric unit" \ "all atoms in PDB file" \ "extent defined by user" ] \ MAP_LIMITS_ALIAS [list INPUT PDB USER ] if { $mode == "INPUT" } { set array(MAP_LIMITS_MODE) "asymmetric unit" } } } #---------------------------------------------------------------- proc PattersonMapmask { arrayname counter } { #----------------------------------------------------------------- SetProgramHelpFile "npo" CreateLine line \ message "Set output axis order for map (AXIS)" \ help sectns \ label "Plot sections on" \ widget SECTION_AXIS \ label "axis from" \ widget F_SECTION \ label "to" \ widget L_SECTION \ label "in steps of" \ widget SKIP_SECTION \ -width 3 } #-------------------------------------------------------------- proc fft_ifpeaksearch { arrayname } { #-------------------------------------------------------------- upvar #0 $arrayname array set array(IFPEAKSEARCK) \ [regexp PEAK [GetValue $arrayname COORDS_MODE] ] } #-------------------------------------------------------------- proc fft_if_mapout { arrayname } { #-------------------------------------------------------------- upvar #0 $arrayname array if { ![regexp MAP [GetValue $arrayname FFTPROGRAM]] || ![regexp CCP4 [GetValue $arrayname FFT_MAP_FORMAT] ] || ![regexp INPUT [GetValue $arrayname MAP_LIMITS_MODE ] ] } { set array(IFMAPOUT) 1 } else { set array(IFMAPOUT) 0 } } #----------------------------------------------------------------------- proc fft_task_window { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "Run FFT - Create Map" "FFT" \ [ list "Define Map" \ "Map Limits" \ "Extending Map" \ "Exclude Reflections" \ "Select Plot Sections" \ "Peak Search Details" \ "Plot Details" \ "Infrequently Used Options" ] ] == 0 } return SetDefaultMapFormat $arrayname FFT_MAP_FORMAT -noxtal SetProgramHelpFile "fft" fft_extent $arrayname fft_if_mapout $arrayname #=PROTOCOL============================================================== OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ message "Use the FFT or input existing map?" \ help description \ widget FFTPROGRAM \ -command "fft_extent $arrayname; fft_if_mapout $arrayname" \ message "Select type of map to generate" \ help labin \ label "to generate" \ widget LABIN \ label "map" CreateLine line \ message "Generate map in alternative format?" \ label "Output map in" \ widget FFT_MAP_FORMAT \ -command "fft_if_mapout $arrayname" \ label "format" \ label "to cover" \ message "Choose criteria to define the extent of the map" \ help xyzlim \ widget MAP_LIMITS_MODE \ -command "fft_if_mapout $arrayname" SetProgramHelpFile "npo" CreateLine line \ message "" \ label "Select hand for phased translation:" \ widget WHICH_HAND \ toggle_display LABIN open [list "phased translation"] CreateLine line \ message "List peaks to PDB file" \ widget IFPEAKSEARCH \ label "Do peak search of map" CreateLine line \ message "Generate postscript file of 2d plots (NPO)?" \ help description \ widget RUN_NPO \ label "Plot" \ label "map sections with " \ message "Display coordinates on plot?" \ widget COORDS_MODE -command "fft_ifpeaksearch $arrayname" #=FILES================================================================ OpenFolder file SetProgramHelpFile "fft" OpenSubFrame frame -toggle_display FFTPROGRAM hide MAP CreateInputFileLine line \ "Enter input MTZ file name (HKLIN)" \ "MTZ in" \ HKLIN DIR_HKLIN \ -fileout MAPOUT DIR_MAPOUT -- \ -fileout O_MAPOUT DIR_O_MAPOUT -- \ -fileout Q_MAPOUT DIR_Q_MAPOUT -- \ -setlabin EXCLUDE_FREER_LABEL [list FREE FreeR FreeR_flag] \ -setfileparam space_group_name SPACE_GROUP \ -setfileparam resolution_min EXCLUDE_RESOLUTION_MIN \ -setfileparam resolution_max EXCLUDE_RESOLUTION_MAX CreateLabinLine line \ "Choose amplitude (F1) and optional sigma (SIG1)" \ HKLIN "F1 " F1 {} \ -sigma "Sigma " SIGF1 {} \ -toggle_display LABIN hide anomalous CreateLabinLine line \ "Choose phase (PHI) and optional weighting factor (W)" \ HKLIN "PHI " PHI {} \ -sigma "Weight " W {} CreateLabinLine line \ "Choose anomalous amplitude (DANO) " \ HKLIN "DANO " DANO {} \ -sigma "Sigma " SIGDANO {} \ -toggle_display LABIN hide \ [list simple nF1-mF2 {vector difference} {double difference} {phased translation}] CreateLabinLine line \ "Choose second amplitude (F2) and optional weighting factor (SIG2)" \ HKLIN "F2 " F2 {} \ -sigma "Sigma " SIG2 {} \ -toggle_display LABIN hide {simple anomalous} CreateLabinLine line \ "Choose second phase (PHI2) and optional weighting factor (W2)" \ HKLIN "PHI2 " PHI2 {} \ -sigma "Weight " W2 {} \ -toggle_display LABIN hide \ [list simple nF1-mF2 anomalous "double difference" ] CreateLabinLine line \ "Choose heavy atom amplitude (FH)" \ HKLIN FH FH FH \ -toggle_display LABIN open { "double difference" } CreateLabinLine line \ "Choose heavy atom phase (PHIH)" \ HKLIN PHIH PHIH PHIH \ -toggle_display LABIN open { "double difference" } CloseSubFrame SetProgramHelpFile "mapmask" CreateInputFileLine line \ "Enter name of input map(MAPMASK XYZIN)" \ "Map in" \ MAPIN DIR_MAPIN \ -fileout O_MAPOUT DIR_O_MAPOUT -- \ -fileout Q_MAPOUT DIR_Q_MAPOUT -- \ -toggle_display FFTPROGRAM open MAP CreateInputFileLine line \ "Enter name of file containing molecule for map to cover (EXTEND XYZIN)" \ "PDB file" \ EXTEND_XYZIN DIR_EXTEND_XYZIN \ -toggle_display MAP_LIMITS_MODE open PDB SetProgramHelpFile "fft" OpenSubFrame frame -toggle_display IFMAPOUT open 1 CreateOutputFileLine line \ "Enter map file name or click file browser icon (MAPOUT)" \ "Map out" \ MAPOUT DIR_MAPOUT \ -toggle_display FFT_MAP_FORMAT open CCP4 CreateOutputFileLine line \ "Enter name for Quanta map file" \ "Quanta map" \ Q_MAPOUT DIR_Q_MAPOUT \ -toggle_display FFT_MAP_FORMAT open QUANTA CreateOutputFileLine line \ "Enter name for O map file" \ "O map" \ O_MAPOUT DIR_O_MAPOUT \ -toggle_display FFT_MAP_FORMAT open O CloseSubFrame CreateOutputFileLine line \ "Enter PDB file name (XYZOUT)" \ "Peak coords" \ XYZPEAKS DIR_XYZPEAKS \ -toggle_display IFPEAKSEARCH open 1 OpenSubFrame frame -toggle_display RUN_NPO open 1 CreateInputFileLine line \ "Enter PDB file name (XYZIN)" \ "Plot coords" \ XYZ_FILE DIR_XYZ_FILE \ -toggle_display COORDS_MODE open [list FILE ] CloseSubFrame #=PARAMETERS========================================================== OpenFolder 1 FFTPROGRAM open [list fft] hide CreateLine line \ message "Scale amplitudes (SCALE) for both datasets" \ help "scale" \ label "For nF1-mF2 map set n=" \ widget SCALE_AMPL_1 \ label "and m=" \ widget SCALE_AMPL_2 \ toggle_display LABIN open [list nF1-mF2 "vector difference" ] CreateLine line \ message "Exclude reflections in set selected for FreeR \ calculation (FREERFLAG&FREE)" \ help freerflag \ widget EXCLUDE_FREER \ label "Exclude set of FreeR reflections defined by MTZ label" \ widget EXCLUDE_FREER_LABEL #===============================================================Map limits OpenFolder 2 MAP_LIMITS_MODE open USER hide SetProgramHelpFile mapmask CreateLine line \ message "Map limits set by user (XYZLIM)" \ help xyzlim \ label "Map extent x" \ widget XYZLIM_1 \ widget XYZLIM_2 \ label "y" \ widget XYZLIM_3 \ widget XYZLIM_4 \ label "z" \ widget XYZLIM_5 \ widget XYZLIM_6 OpenFolder 3 MAP_LIMITS_MODE open PDB hide CreateLine line \ message "Border in Angstrom around atoms in coordinate file (MAPMASK BORDER)" \ label "Border in Angstrom around atoms" \ widget BORDER SetProgramHelpFile fft #=EXCLUDE=REFLECTIONS====================================================== OpenFolder 4 FFTPROGRAM hide MAP closed CreateLine line \ message "Exclude reflections below and/or above resolution limit in \ Angstrom (RESOLUTION)" \ help resolution \ widget EXCLUDE_RESOLUTION \ -toggleon \ label "Resolution less than" \ widget EXCLUDE_RESOLUTION_MIN \ label "A or greater than" \ widget EXCLUDE_RESOLUTION_MAX \ label "A" ############################################## # EXCLUDE for F1 and F2 ############################################## CreateLineTemplate "EXCLUDE" [list 0.0 0.6 0.8] OpenSubFrame frame -toggle_display LABIN hide { simple anomalous } CreateLine line \ label "Exclude reflections: parameters for " \ -italic \ label "F1 and" \ -italic \ label "F2" \ -italic \ format template "EXCLUDE" CreateLine line \ message "Exclude reflections with Fs which are small compared to sigma F" \ help excl_sig \ widget EXCLUDE_BYSIGMA \ -toggleon \ label "F less than n * sigmaF where n is " \ widget EXCLUDE_BYSIGMA_1 \ widget EXCLUDE_BYSIGMA_2 \ format template "EXCLUDE" CreateLine line \ message "Exclude reflections with small absolute values" \ help excl_min \ widget EXCLUDE_MINIMUM \ -toggleon \ label "F absolute value less than " \ widget EXCLUDE_MINIMUM_1 \ widget EXCLUDE_MINIMUM_2 \ format template "EXCLUDE" CreateLine line \ message "Exclude reflections with large absolute values" \ help excl_max \ widget EXCLUDE_MAXIMUM \ -toggleon \ label "F absolute value greater than " \ widget EXCLUDE_MAXIMUM_1 \ widget EXCLUDE_MAXIMUM_2 \ format template "EXCLUDE" CreateLine line \ message "Exclude reflections with large differences between F1 and F2" \ help excl_diff \ widget EXCLUDE_BYDIFF \ -toggleon \ label "Difference between F1 and F2 greater than" \ widget EXCLUDE_BYDIFF_DIFF \ format template "EXCLUDE" CloseSubFrame ############################################## # EXCLUDE for F1 only ############################################## CreateLineTemplate "EXCLUDE1" [list 0.0 0.6] OpenSubFrame frame -toggle_display LABIN open { simple anomalous } CreateLine line \ label "Exclude reflections: parameters for " \ -italic \ label "F1" \ -italic \ format template "EXCLUDE1" CreateLine line \ message "Exclude reflections with Fs which are small compared to sigma F" \ help excl_sig \ widget EXCLUDE_BYSIGMA \ -toggleon \ label "F less than n * sigmaF where n is " \ widget EXCLUDE_BYSIGMA_1 \ format template "EXCLUDE1" CreateLine line \ message "Exclude reflections with small absolute values" \ help excl_min \ widget EXCLUDE_MINIMUM \ -toggleon \ label "F absolute value less than " \ widget EXCLUDE_MINIMUM_1 \ format template "EXCLUDE1" CreateLine line \ message "Exclude reflections with large absolute values" \ help excl_max \ widget EXCLUDE_MAXIMUM \ -toggleon \ label "F absolute value greater than " \ widget EXCLUDE_MAXIMUM_1 \ format template "EXCLUDE1" #CreateLine line \ # message "Exclude reflections with large differences between F1 and F2" \ # help excl_diff \ #widget EXCLUDE_BYDIFF \ #-toggleon \ #label "Difference between F1 and F2 greater than" \ #widget EXCLUDE_BYDIFF_DIFF \ #format template "EXCLUDE" CloseSubFrame #=Unusual Options======================================================== OpenFolder 8 FFTPROGRAM hide MAP closed CreateLine line \ message "Space group (default as in MTZ file) (FFTSPACEGROUP)" \ label "Generate map in space group" \ help fftspacegroup \ widget FFT_SPACE_GROUP CreateLine line \ message "Exclude reflections in set selected for FreeR \ calculation (FREE)" \ label "Exclude reflections in FreeR set with value" \ widget EXCLUDE_FREER_VALUE CreateLine line \ message "Scale map amplitudes, enter cell volume and F000" \ help vf000 \ widget SCALE_MAP \ -toggleon \ label "Scale map using cell volume" \ widget SCALE_VOLUME \ label "and F000" \ widget SCALE_F000 CreateLine line \ message "Apply scaling to B-factors" \ help scale_bfac \ widget BFACTOR_SCALING \ -toggleon \ label "Apply B-factor scaling to F1" \ widget SCALE_BFACTOR_1 \ toggle_display LABIN open { simple anomalous } CreateLine line \ message "Apply scaling to B-factors" \ help scale_bfac \ widget BFACTOR_SCALING \ -toggleon \ label "Apply B-factor scaling to F1" \ widget SCALE_BFACTOR_1 \ label " and F2" \ widget SCALE_BFACTOR_2 \ toggle_display LABIN hide { simple anomalous } CreateLine line \ message "Override default grid spacing" \ help grid \ widget GRID \ -toggleon \ label "Grid spacing x= " \ widget GRID_1 \ label " y= " \ widget GRID_2 \ label " z= " \ widget GRID_3 CreateLine line \ message "Change axis order in output file (AXIS)" \ help axis \ widget IFAXIS \ label "Change axis order to" \ widget AXIS #-----------------------------------------------------------plot sections OpenFolder 5 RUN_NPO open 1 hide SetProgramHelpFile npo CreateLine line \ message "Define sections in fractional or grid coordinates (SECTION)" \ help section \ widget SECTION_FRAC \ label "Define sections in fractional coordinates" CreateExtendingFrame N_SECTIONS PattersonMapmask \ "Specify sections to plot" \ "Add sections" \ [list SECTION_AXIS \ F_SECTION \ L_SECTION \ SKIP_SECTION ] CreateLine line \ message "Contour levels for map plot (CONTRS)" \ help group2_contrs \ label "Map contour levels entered as a" \ widget CONTOUR_MODE \ label "of" \ widget CONTOUR_PARAM CreateLine line \ message "Enter list of contouring levels (max of 6) (CONTRS)" \ help group2_contrs \ label "Contour levels" \ widget CONTOUR_LIST_1 \ widget CONTOUR_LIST_2 \ widget CONTOUR_LIST_3 \ widget CONTOUR_LIST_4 \ widget CONTOUR_LIST_5 \ widget CONTOUR_LIST_6 \ label "and" \ widget PLOT_NEG \ label "negative values" \ toggle_display CONTOUR_MODE hide range CreateLine line \ message "Enter range of contour levels (CONTRS)" \ help group2_contrs \ label "Contour levels from" \ widget CONTOUR_RANGE_1 \ label "to" \ widget CONTOUR_RANGE_2 \ label "by intervals of" \ widget CONTOUR_RANGE_STEP \ label "and" \ widget PLOT_NEG \ label "negative values" \ toggle_display CONTOUR_MODE hide list #-----------------------------------------------------------Peaksearch OpenFolder 6 IFPEAKSEARCH open 1 hide SetProgramHelpFile "peakmax" CreateLine line \ label "Coordinates of peaks will be saved in coordinate file & plotted" \ -italic CreateLine line \ message "Create fractional coordinate file (OUTPUT FRAC)" \ help output \ widget IFFRACOUT \ label "Also output peaks in fractional coordinates" CreateLine line \ message "Set criteria for peaks search (THRESHOLD NEGATIVES)" \ help threshhold \ label "Search for peaks greater than" \ widget THRESHHOLD \ label "sigma " \ widget NEGATIVES \ label "Search for negative peaks" CreateLine line \ message "Maximum number of peaks (NUMPEAKS)" \ label "Number of peaks output to list " \ widget NUMPEAKS CreateLine line \ message "Define format of ATOM card in output PDB file" \ label "PDB ATOM card with chain" \ widget CHAIN \ -width 4 \ label "residue" \ widget RESIDUE \ -width 6 \ label "atom" \ widget ATNAME \ -width 6 \ label "Bfactor" \ widget BFACTOR \ -width 6 \ label "occupancy" \ widget OCCUPANCY \ -width 6 #run NPO================================================================ OpenFolder 7 RUN_NPO hide 0 closed SetProgramHelpFile "npo" CreateLine line \ message "Set a maximum plot size for scale to calculated automatically" \ help group2_map_scale \ label "Set maximum plot size" \ widget NPO_MAX_SIZE \ label "cms Or define plot scale" \ message "Set scale of plot (MAP SCALE)" \ widget NPO_SCALE \ label "mm/A Character size" \ widget NPO_CHAR_SIZE CreateLine line \ message "Enter colour for plotting heavy atoms (RESIDU)" \ help group4_colour \ label "Colour atoms/vectors" \ widget NPO_ATOM_COLOUR \ label " " \ help group3_label \ widget NPO_LABELS \ label "atoms" CreateLine line \ message "Define grid spacing and offset (GRID)" \ help group2_grid \ widget GRID_PLOT_MODE \ label "Plot grid with spacing (" \ widget GRID_PLOT_UNITS \ label ") in u" \ widget NPO_GRID_1 \ -width 5 \ label "and v" \ widget NPO_GRID_2 \ -width 5 \ label "& offset in u" \ widget NPO_GRID_3 \ -width 5 \ label "and v" \ widget NPO_GRID_4 \ -width 5 }