# # 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 $Id$ # ====================================================================== # mapave.tcl -- # # Run maprot to generate averaged map # # CCP4Interface # # ====================================================================== #----------------------------------------------------------------------- proc ncs_operators { arrayname counter } { #----------------------------------------------------------------------- CreateLine ops_frame \ message "Enter NCS operator (NCSROT POLAR)" \ label "alpha" \ widget NCS_OP_ALPHA \ label "beta" \ widget NCS_OP_BETA \ label "gamma" \ widget NCS_OP_GAMMA \ label "xtran" \ widget NCS_OP_XTRAN \ label "ytran" \ widget NCS_OP_YTRAN \ label "ztran" \ widget NCS_OP_ZTRAN } #----------------------------------------------------------------------- proc rsps_setup { typedefVar arrayname } { #----------------------------------------------------------------------- DefineMenu _rsps_score_mode [ list "sum function" \ "product function" \ "harmonic mean function" ] \ [ list SUM PRODUCT HARMONIC ] DefineMenu _rsps_input [ list "read from coordinate file" \ "from scan of Patterson map" ] \ [ list FILE SCAN ] DefineMenu _rsps_mode [ list "do nothing" \ "find sets of sites with good cross vectors" \ "find sites with good cross vectors to fixed site(s)" ] \ [ list NOTHING GETSETS CROSSPEAKS ] return 1 } #----------------------------------------------------------------------- proc rsps_run { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array set input [GetValue $arrayname RSPS_INPUT] set mode [GetValue $arrayname RSPS_MODE] set array(INPUT_FILES) PATFILE set array(OUTPUT_FILES) "" if [StringSame $input FILE] { for { set n 1 } { $n <= $array(NINSITESFILE) } { incr n } { append array(INPUT_FILES) " " INSITESFILE,$n } } else { append array(OUTPUT_FILES) HPEAKSFIL set array(NINSITESFILE) 1 set array(INSITESFILE,1) $array(HPEAKSFIL) } if [StringSame $mode CROSSPEAKS] { append array(OUTPUT_FILES) " " XPEAKSFIL } return 1 } #----------------------------------------------------------------------- proc rsps_insites { arrayname counter } { #----------------------------------------------------------------------- CreateInputFileLine line \ "Enter input potential heavy atom sites (HPEAKSFIL)" \ "Sites in" INSITESFILE DIR_INSITESFILE } #----------------------------------------------------------------------- proc rsps_task_window { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "RSPS - Real Space Patterson Search" "RSPS" \ [ list "Essential Parameters" \ "Scan Patterson for Potential Vectors" \ "Find Sets of Sites with Good Cross Vectors" \ "Find Sites with Good Cross Vectors to Fixed Site(s)" \ "Non-Crystallographic Symmetry Operators" \ "Search Extent" ] ] == 0 } return SetProgramHelpFile rsps #=PROTOCOL============================================================== OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ label "Get list of potential heavy atom sites" \ widget RSPS_INPUT CreateLine line \ label "To analyse sites" \ widget RSPS_MODE #=FILES================================================================ OpenFolder file CreateInputFileLine line \ "Enter input Patterson map file name (PATFILE)" \ "Map in" PATFILE DIR_PATFILE \ -setfileparam xyzlim XYZLIM CreateOutputFileLine line \ "Save potential heavy atom sites in pseudo-PDB file (HPEAKSFIL)" \ "Sites out" HPEAKSFIL DIR_HPEAKSFIL \ -toggle_display RSPS_INPUT open SCAN OpenSubFrame frame -toggle_display RSPS_INPUT open FILE CreateExtendingFrame NINSITESFILE rsps_insites \ "Add name of file contains putative HA sites." \ "Add sites file" \ [ list INSITESFILE DIR_INSITESFILE] CloseSubFrame OpenSubFrame frame -toggle_display RSPS_MODE open CROSSPEAKS CreateLine line \ label "Root name for file(s) listing Harker peaks for cross vectors" \ -italic CreateOutputFileLine line \ "Enter name for cross-peaks pseudo-PDB coordinates file (XPEAKSFIL)" \ "Peaks out" XPEAKSFIL DIR_XPEAKSFIL CloseSubFrame #--------------------------------------------------------------Essential OpenFolder 1 CreateLine line \ message "Space group (default as in map file) (SYMMETRY)" \ help spacegroup \ label "Crystal (not Patterson) space group" \ widget SPACE_GROUP -oblig #------------------------------------------------------------harker scan OpenFolder 2 RSPS_INPUT closed SCAN hide CreateLine line \ label "Find" \ widget PICK_HARKER_N \ label "potential vectors" CreateLine line \ label "Pick vectors correlating to peaks >" \ message "Leave blank for default reject criteria of 1 sigma (REJECT)" \ widget HARKER_REJECT \ label "sigma in map allowing" \ message "Allow n peaks per vectors to be below rejection criteria (LOW)" \ widget HARKER_LOW \ label "peak(s) below threshold" # -----------------------------------------------------------getsets OpenFolder 3 RSPS_MODE closed GETSETS hide CreateLine line \ label "Find sets of at least" \ widget GETSETS_MIN \ label "sites from the first" \ widget GETSETS_USE \ label "in list of potential sites" CreateLine line \ label "Pick sites correlating to peaks >" \ message "Leave blank for default reject criteria of 1 sigma (REJECT)" \ widget GETSETS_REJECT \ label "sigma in map allowing" \ message "Allow n peaks per site to be below rejection criteria (LOW)" \ widget GETSETS_LOW \ label "peak(s) below threshold" #-----------------------------------------------------------cross peaks OpenFolder 4 RSPS_MODE closed CROSSPEAKS hide CreateLine line \ label "Set each of the best" \ widget N_CROSS_PEAKS \ label "sites as fixed in turn" CreateLine line \ label "Find" \ widget PICK_CROSS_N \ label "sites giving best cross vectors" \ label "and list Harker vectors for" \ widget X_LIST_HARKER_N \ label "best sites" CreateLine line \ label "Pick sites correlating to peaks >" \ message "Leave blank for default reject criteria of 1 sigma (REJECT)" \ widget CROSS_REJECT \ label "sigma in map allowing" \ message "Allow n peaks per site to be below rejection criteria (LOW)" \ widget CROSS_LOW \ label "peak(s) below threshold" CreateLine line \ label "Score cross peaks using" \ message "Scoring function (SCORE)" \ widget CROSS_SCAN_SCORE_MODE \ label "applied to" \ message "Leave blank for default to apply to all peaks (SCORE)" \ widget CROSS_SCAN_SCORE_N \ label "smallest peaks" #------------------------------------------------------------NCS operators OpenFolder 5 closed CreateExtendingFrame NCS_NOPS ncs_operators \ "Add/remove line to define NCS symmetry (identity NOT needed)" \ "Add NCS operator" \ [ list NCS_OP_ALPHA \ NCS_OP_BETA \ NCS_OP_GAMMA \ NCS_OP_XTRAN \ NCS_OP_YTRAN \ NCS_OP_ZTRAN ] #---------------------------------------------------------map parameters OpenFolder 6 closed CreateLine line \ message "Change map search limits, default is asymmetric unit (LIMITS)" \ help scan \ widget IFXYZLIM \ -toggleon \ label "Search 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 # CreateLine line \ # message "Set grid values (GRID)" \ # help grid \ # label "Grid x=" \ # widget GRID_1 \ # label "y=" \ # widget GRID_2 \ # label "z=" \ # widget GRID_3 }