# # 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 $Id$ # ====================================================================== # maputils.tcl -- # # Run mapmask for map/mask utilities # maprot for interpolation and rotation # # CCP4Interface # # ====================================================================== #----------------------------------------------------------------------- proc maputils_setup { typedefVar arrayname } { #----------------------------------------------------------------------- DefineMenu _mapmask_mode [ list "Edit a map/mask file" \ "Extend a map/mask file" \ "Print a map/mask file" \ "Interpolate map to alternative grid" \ "Rotate map" \ "Create mask from map" \ "Scale map using a mask" \ "Solvent flatten a map using a mask" \ "Combine maps/masks" ] \ [ list EDIT \ EXTEND \ PRINT \ INTERPOLATE \ ROTATE \ CREATE_MASK \ SCALE_BY_MASK \ SOLVENT_FLATTEN \ COMBINE ] DefineMenu _mapmask_which [ list "map" "mask" ] \ [ list MAP MASK ] DefineMenu _mapmask_which_1 [ list "two map files" \ "two mask files" \ "a map and a mask" ] \ [ list MAP MASK BOTH ] DefineMenu _mapmask_ext_mode [ list "cover all atoms in molecule" \ "asymmetric unit" \ "unit cell" \ "same extent as another map" \ "extent defined by user" ] \ [ list MOLECULE ASU CELL MATCH USER ] DefineMenu _mapmask_extend [ list "applying program default" \ "copying density" \ "applying symmetry" \ "overlapping copy & symmetry" ] \ [list DEFAULT \ COPY \ XTAL \ OVERLAP ] DefineMenu _mapmask_mask [ list "density above cutoff" \ "fraction of output mask" \ "fraction of unit cell" ] \ [ list CUT FRAC VOLUME ] DefineMenu _mapmask_scale_1 [ list "by applying scale factor" \ "to set mean and SD" ] \ [ list FACTOR SIGMA ] DefineMenu _mapmask_scale_2 [ list "mean for protein and solvent" \ "ratio of SD/mean for protein" ] \ [ list MEAN RATIO ] DefineMenu _mapmask_flip [ list "flattening" "flipping" ] \ [ list "1.0" "2.0" ] DefineMenu _mapmask_combine [ list addition multiplication ] \ [ list ADD MULT ] return 1 } #----------------------------------------------------------------------- proc maputils_run { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array set array(IFMAPROT) 0 set array(IFXYZLIM) 0 set array(XYZLIM_MODE) "" set array(IFBORDER) 0 set array(IFMASK) 0 set array(IFSOLVENT_FLAT) 0 set array(IFCOMBINE) 0 set array(INPUT_FILES) "" set array(OUTPUT_FILES) "" set mode [GetValue $arrayname MAPMASK_MODE] set ifmap [regexp MAP [GetValue $arrayname MAPMASK_OBJECT]] set array(SPACE_GROUP) [GetSpaceGroupNumber $array(SPACE_GROUP)] if { ![StringSame $mode EDIT]} { set array(IFAXIS) 0 } if { ![StringSame $mode EXTEND]} { set array(IFPAD) 0 } if { ![StringSame $mode PRINT EDIT ]} { set array(IFSCALE) 0 } if { ![StringSame $mode CREATE_MASK ]} { set array(IFPRINT) 0 } if [StringSame $mode PRINT] { set array(SCALE_MODE) [GetValue $arrayname SCALE_MODE_1] set array(IFPRINT) 1 if $ifmap { set array(INPUT_FILES) MAPIN } \ else { set array(INPUT_FILES) MSKIN } } elseif [StringSame $mode EXTEND ] { if $ifmap { set array(INPUT_FILES) MAPIN; set array(OUTPUT_FILES) MAPOUT } \ else { set array(INPUT_FILES) MSKIN; set array(OUTPUT_FILES) MSKOUT } switch [GetValue $arrayname EXTEND_FUNCTION] \ USER { set array(IFXYZLIM) 1 } MOLECULE { lappend array(INPUT_FILES) XYZIN set array(IFBORDER) 1 } MATCH { lappend array(INPUT_FILES) MAPLIM set array(XYZLIM_MODE) MATCH } CELL { set array(XYZLIM_MODE) CELL } ASU { set array(XYZLIM_MODE) ASU } } elseif [StringSame $mode EDIT ] { set array(SCALE_MODE) [GetValue $arrayname SCALE_MODE_1] if $ifmap { set array(INPUT_FILES) MAPIN; set array(OUTPUT_FILES) MAPOUT } \ else { set array(INPUT_FILES) MSKIN; set array(OUTPUT_FILES) MSKOUT } } elseif [StringSame $mode INTERPOLATE ROTATE ] { set array(IFMAPROT) 1 set array(INPUT_FILES) MAPIN; set array(OUTPUT_FILES) MAPOUT set array(IFXYZLIM) 1 } elseif [StringSame $mode CREATE_MASK] { set array(IFMASK) 1 if $array(IFPRINT) { set array(MAPMASK_OBJECT) MASK} set array(INPUT_FILES) MAPIN set array(OUTPUT_FILES) MSKOUT } elseif [StringSame $mode SCALE_BY_MASK] { set array(IFSCALE) 1 set array(SCALE_MODE) [GetValue $arrayname SCALE_MODE_2] set array(INPUT_FILES) [list MAPIN MSKIN2] set array(OUTPUT_FILES) MAPOUT } elseif [StringSame $mode SOLVENT_FLATTEN] { set array(IFSOLVENT_FLAT) 1 set array(INPUT_FILES) [list MAPIN MSKIN2] set array(OUTPUT_FILES) MAPOUT } elseif [StringSame $mode COMBINE ] { set array(IFCOMBINE) 1 if $ifmap { set array(INPUT_FILES) [list MAPIN MAPIN2] set array(OUTPUT_FILES) MAPOUT } else { set array(INPUT_FILES) [list MSKIN MSKIN2] set array(OUTPUT_FILES) MSKOUT } } return 1 } #----------------------------------------------------------------------- proc maputils_input_files { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array set array(IMAP1) 0 set array(IMAP2) 0 set array(IMASK1) 0 set array(IMASK2) 0 set array(OMAP) 0 set array(OMASK) 0 set mode [GetValue $arrayname MAPMASK_MODE] set object [GetValue $arrayname MAPMASK_OBJECT] if [StringSame $mode EDIT EXTEND ] { if [StringSame $object MAP ] { set array(IMAP1) 1 set array(OMAP) 1 } else { set array(IMASK1) 1 set array(OMASK) 1 } } elseif [StringSame $mode INTERPOLATE ROTATE ] { set array(IMAP1) 1 set array(OMAP) 1 } elseif [StringSame $mode PRINT ] { if [regexp MAP $object ] { set array(IMAP1) 1 } else { set array(IMASK1) 1 } } elseif [StringSame $mode CREATE_MASK ] { set array(IMAP1) 1 set array(OMASK) 1 } elseif [StringSame $mode SCALE_BY_MASK SOLVENT_FLATTEN ] { set array(IMAP1) 1 set array(IMASK2) 1 set array(OMAP) 1 } elseif [StringSame $mode COMBINE ] { if [StringSame $object MAP ] { set array(IMAP1) 1 set array(IMAP2) 1 set array(OMAP) 1 } else { set array(IMASK1) 1 set array(IMASK2) 1 set array(OMASK) 1 } } } #----------------------------------------------------------------------- proc mapmask_scale { arrayname } { #----------------------------------------------------------------------- # Draw the scale lines since will be used in several context CreateLine line \ message "Scale density by scale factors or by setting mean&SD (SCALE FACTOR/SIGMA)" \ help scale \ widget IFSCALE \ label "Scale density" \ widget SCALE_MODE_1 \ label "Multiply density by" \ message " " \ widget SCALE_FACTOR_1 \ label "and add" \ widget SCALE_FACTOR_2 \ toggle_display SCALE_MODE_1 open FACTOR CreateLine line \ message "Scale density by scale factors or by setting mean&SD (SCALE FACTOR/SIGMA)" \ help scale \ widget IFSCALE \ label "Scale the map" \ widget SCALE_MODE_1 \ label "Scale density to have SD" \ message " " \ widget SCALE_SIGMA_1 \ label "and mean" \ widget SCALE_SIGMA_2 \ toggle_display SCALE_MODE_1 hide FACTOR } #----------------------------------------------------------------------- proc maputils_task_window { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "Edit/Rotate Map & Mask" "Map Utilities" \ [ list "Print File" \ "Edit File" \ "Extend File" \ "Interpolate Map to Different Grid" \ "Rotate Map" \ "Create Mask from Map" \ "Scale Map Using a Mask" \ "Solvent Flatten a Map" \ "Combine Maps/Masks" \ "Cell Parameters" ] ] == 0 } return SetProgramHelpFile mapmask #=PROTOCOL============================================================== OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ message "Use mapmask to perform which function" \ help keywords \ widget MAPMASK_MODE \ -command "maputils_input_files $arrayname" \ toggle_display MAPMASK_MODE hide [list EDIT EXTEND PRINT COMBINE ] CreateLine line \ message "Use mapmask to perform which function" \ help keywords \ widget MAPMASK_MODE \ -command "maputils_input_files $arrayname" \ label "for a" \ widget MAPMASK_OBJECT \ -command "maputils_input_files $arrayname" \ label "file" \ toggle_display MAPMASK_MODE open [list EDIT EXTEND PRINT ] CreateLine line \ message "Use mapmask to perform which function" \ help keywords \ widget MAPMASK_MODE \ -command "maputils_input_files $arrayname" \ label "for" \ widget MAPMASK_OBJECT \ -command "maputils_input_files $arrayname" \ label "files" \ toggle_display MAPMASK_MODE open [list COMBINE ] #=FILES================================================================ OpenFolder file CreateInputFileLine line \ "Enter input map file name (MAPIN)" \ "Map in" \ MAPIN DIR_MAPIN \ -fileout MAPOUT DIR_MAPOUT _1 \ -setfileparam space_group_number SPACE_GROUP \ -setfileparam cell CELL \ -setfileparam grid GRID \ -setfileparam xyzlim XYZLIM \ -toggle_display IMAP1 open 1 CreateInputFileLine line \ "Enter input map file name (MAPIN2)" \ "Map in" \ MAPIN2 DIR_MAPIN2 \ -toggle_display IMAP2 open 1 CreateInputFileLine line \ "Enter input mask file name (MSKIN)" \ "Mask in" \ MSKIN DIR_MSKIN \ -fileout MSKOUT DIR_MSKOUT _1 \ -toggle_display IMASK1 open 1 CreateInputFileLine line \ "Enter input mask file name (MSKIN2)" \ "Mask in" \ MSKIN2 DIR_MSKIN2 \ -toggle_display IMASK2 open 1 # OpenSubFrame frame -toggle_display MAPMASK_MODE open [list INTERPOLATE ROTATE ] # # CreateLine line \ # label "Read crystal parameters from MTZ file:" -italic # # CreateInputFileLine line \ # "Enter name of MTZ file containing cell and space group info" \ # "MTZ file" \ # MTZIN DIR_MTZIN \ # -setfileparam space_group_name SPACE_GROUP \ # -setfileparam cell CELL # # CloseSubFrame CreateOutputFileLine line \ "Enter map file name or click file browser icon (MAPOUT)" \ "Map out" \ MAPOUT DIR_MAPOUT \ -toggle_display OMAP open 1 CreateOutputFileLine line \ "Enter mask file name or click file browser icon (MSKOUT)" \ "Mask out" \ MSKOUT DIR_MSKOUT \ -toggle_display OMASK open 1 #--------------------------------------------------------------print OpenFolder 1 MAPMASK_MODE open PRINT hide CreateLine line \ message "Print sections to log file (PRINT)" \ help print \ label "Print sections along" \ widget PRINT_AXIS \ -toggleon \ label "axis from section" \ widget PRINT_FIRST \ label "to section" \ widget PRINT_LAST \ label "in steps of" \ widget PRINT_STEP mapmask_scale $arrayname #--------------------------------------------------------------edit OpenFolder 2 MAPMASK_MODE open EDIT hide CreateLine line \ message "Change space group record in map/mask file (SYMMETRY)?" \ help symmetry \ label "Space group" \ widget SPACE_GROUP CreateLine line \ message "Change axis order in output file (AXIS)" \ help axis \ widget IFAXIS \ label "Change axis order to" \ widget AXIS mapmask_scale $arrayname #--------------------------------------------------------------extend OpenFolder 3 MAPMASK_MODE open EXTEND hide CreateLine line \ message "Extend map to asym unit, cover molecule or defined volume? (XYZLIM,BORDER)" \ help extend \ label "Extend map to" \ widget EXTEND_FUNCTION OpenSubFrame frame -toggle_display EXTEND_FUNCTION open MOLECULE CreateInputFileLine line \ "Enter name of file containing molecule coordinates (XYZIN)" \ "PDB file" \ XYZIN DIR_XYZIN CreateLine line \ message "Extend map beyond the molecule for BORDER Angstrom" \ help border \ label "Border around molecule" \ widget BORDER CloseSubFrame OpenSubFrame frame -toggle_display EXTEND_FUNCTION open MATCH CreateInputFileLine line \ "Enter name of map file of required extent (MAPLIM)" \ "Map file" \ MAPLIM DIR_MAPLIM CloseSubFrame 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 \ toggle_display EXTEND_FUNCTION open USER CreateLine line \ message "Default: copy if output map within input; use symmetry if map extended (EXTEND)" \ help extend \ label "Extend map by" \ widget EXTEND_MODE \ label "and" \ message "For map which does not contain asym unit set fixed density in unknown region (PAD)" \ help pad \ widget IFPAD \ label "pad with value" \ widget PADRHO \ label "where density unknown" #--------------------------------------------------------------create mask OpenFolder 6 MAPMASK_MODE open CREATE_MASK hide CreateLine line \ message "Select criteria for mask boundary (MASK)" \ help mask \ label "Select mask for" \ widget MASKMODE \ message "Cutoff density value (MASK CUT mskcit)" \ widget MASKCUT \ toggle_display MASKMODE open CUT CreateLine line \ message "Select criteria for mask boundary (MASK)" \ help mask \ label "Select mask for" \ widget MASKMODE \ message "Fraction of output mask that should be above threshold (MASK FRAC mskfrc )" \ widget MASKFRAC \ toggle_display MASKMODE open FRAC CreateLine line \ message "Select criteria for mask boundary (MASK)" \ help mask \ label "Select mask for" \ widget MASKMODE \ message "Fraction of unit cell above threshold (MASK VOLUME mskvol)" \ widget MASKVOLUME \ toggle_display MASKMODE open VOLUME CreateLine line \ message "Print sections to log file (PRINT)" \ help print \ widget IFPRINT \ -toggleon \ label "Print sections along" \ widget PRINT_AXIS \ label "axis from section" \ widget PRINT_FIRST \ label "to section" \ widget PRINT_LAST \ label "in steps of" \ widget PRINT_STEP #--------------------------------------------------------------scale by mask OpenFolder 7 MAPMASK_MODE open SCALE_BY_MASK hide CreateLine line \ message "Choose how to use mask to scale density (SCALE MEAN/RATIO)" \ help scale \ label "Scale density by setting" \ widget SCALE_MODE_2 \ label "Mean density: protein region" \ widget SCALE_MEAN_1 \ label "solvent region" \ widget SCALE_MEAN_2 \ toggle_display SCALE_MODE_2 open MEAN CreateLine line \ message "Choose how to use mask to scale density (SCALE MEAN/RATIO)" \ help scale \ label "Scale density by setting" \ widget SCALE_MODE_2 \ label "Protein density: SD is" \ widget SCALE_RATIO \ label "of the mean" \ toggle_display SCALE_MODE_2 open RATIO #--------------------------------------------------------------solvent flatten OpenFolder 8 MAPMASK_MODE open SOLVENT_FLATTEN hide CreateLine line \ message "Outside mask density shift multiplied by 1(flattening) or 2(flipping) (SOLV FLIP flipfac)" \ help solv \ label "Perform solvent" \ widget SOLVENT_FLIP_FACTOR \ label "in solvent region" CreateLine line \ message "Attenuate negative density inside the mask (SOLV ATTN attn)" \ help solv \ label "Multiply negative density in protein region by" \ widget SOLVENT_ATTN_FACTOR #--------------------------------------------------------------combine OpenFolder 9 MAPMASK_MODE open COMBINE hide CreateLine line \ message "Combine two maps/masks by addition/multiplication (COMBINE)" \ help maps \ label "Combine maps/masks by" \ widget COMBINE_FUNCTION #---------------------------------------------------------interpolate OpenFolder 4 MAPMASK_MODE open INTERPOLATE hide SetProgramHelpFile maprot CreateLine line \ message "Choose new grid values (GRID)" \ help grid \ label "Grid x=" \ widget GRID_1 \ label "y=" \ widget GRID_2 \ label "z=" \ widget GRID_3 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 #---------------------------------------------------------rotate OpenFolder 5 MAPMASK_MODE open ROTATE hide CreateLine line \ label "Rotation operator - Euler angles" -italic CreateLine ops_frame \ message "Enter Averaging Operator (ROTA EULER & TRAN)" \ label "alpha" \ widget NCS_OP_ALPHA,1 \ label "beta" \ widget NCS_OP_BETA,1 \ label "gamma" \ widget NCS_OP_GAMMA,1 \ label "xtran" \ widget NCS_OP_XTRAN,1 \ label "ytran" \ widget NCS_OP_YTRAN,1 \ label "ztran" \ widget NCS_OP_ZTRAN,1 \ CreateLine line \ label "Create new map with.." -italic CreateLine line \ message "Choose new grid values (GRID)" \ help grid \ label "Grid x=" \ widget GRID_1 \ label "y=" \ widget GRID_2 \ label "z=" \ widget GRID_3 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 #------------------------------------------------------------------cell params OpenFolder 10 MAPMASK_MODE open [list INTERPOLATE ROTATE ] hide CreateLine line \ message "Space group (SYMMETRY)" \ label "Generate map in space group" \ help symmetry \ widget SPACE_GROUP CreateLine line \ message "Cell dimensions (default from map file) (CELL)" \ help "cell" \ label "Set cell a" \ widget CELL_1 -width 8 \ label "b" \ widget CELL_2 -width 8 \ label "c" \ widget CELL_3 -width 8 \ label "alpha" \ widget CELL_4 -width 8 \ label "beta" \ widget CELL_5 -width 8 \ label "gamma" \ widget CELL_6 -width 8 maputils_input_files $arrayname }