# ======================================================================= # phaser_MR.tcl -- # # Maximum Likelihood Molecular Replacement # # CCP4Interface # # ======================================================================= #------------------------------------------------------------------------ proc phaser_MR_setup { typedefVar arrayname } { #------------------------------------------------------------------------ upvar #0 $typedefVar typedef upvar #0 $arrayname array DefineMenu _phaser_mode_mr [list "automated search" \ "rotation search" \ "translation search" \ "refinement and phasing" \ "log-likelihood gain rescoring" \ "packing" \ "anisotropy correction" \ "cell content analysis" ] \ [list "AUTO" \ "ROTATE" \ "TRANSLATE" \ "REFINE" \ "RESCORE" \ "PACK" \ "ANISOTROPY" \ "CONTENT" ] DefineMenu _phaser_mode_rot \ [list "fast rotation function" "brute force ML RF" ] [list "MR_FRF" "MR_BRF"] DefineMenu _phaser_mode_tran \ [list "fast translation function" "brute force ML TF" ] [list "MR_FTF" "MR_BTF" ] DefineMenu _phaser_spacegroup_option \ [list "the mtz space group" "the mtz space group and enantiomorph (if applicable)" "alternative space group(s)" "all choices of alternative space group" ] \ [list "SG_MTZ" "SG_ENANT" "SG_ALT" "SG_ALL" ] DefineMenu _phaser_protnucleic \ [list "protein" "nucleic acid" ] [list "PROTEIN" "NUCLEIC" ] DefineMenu _phaser_rms_option \ [list "rms difference" "sequence identity" ] [list "RMS" "IDENT" ] set typedef(_phaser_ensemble_menu) \ { varmenu ENSEMBLE_MENU_LIST ENSEMBLE_MENU_ALIAS 15 } DefineMenu _phaser_brf_search_option \ [list "full" "around" ] [list "FULL" "AROUND" ] DefineMenu _phaser_btf_search_option \ [list "full" "around" "region" "line" "degenerate" ] \ [list "FULL" "AROUND" "REGION" "LINE" "DEGENERATE"] DefineMenu _phaser_ensemble_option \ [list "pdb file(s)" "mtz file" ] [list "PDB" "MTZ"] set typedef(_phaser_comp_option) \ { menu { "molecular weight" "sequence file" } { "MW" "FASTA" } } set typedef(_phaser_tra_entry_option) \ { menu { "manually" "from .rlist file" } { "MANUAL" "FILE" } } set typedef(_phaser_frf_target_option) \ { menu { "LERF1" "LERF2" "Crowther" } { "LERF1" "LERF2" "CROWTHER" } } set typedef(_phaser_ftf_target_option) \ { menu { "LETF1" "Correl" } { "LETF1" "CORREL" } } set typedef(_phaser_coord_sys) \ { menu { "orthogonal" "fractional" } { "ORTHOGONAL" "FRACTIONAL" } } DefineMenu _phaser_plane_option \ [list "XY" "XZ" "YZ" ] [list "XY" "XZ" "YZ"] set typedef(_phaser_rescore_option) \ { menu { "sigma cutoff" "number of peaks" "percentage of top peak" "all peaks" } \ { "SIGMA" "NPEAKS" "PERCENT" "ALL" } } set typedef(_phaser_save_option) \ { menu { "sigma cutoff" "number of peaks" "percentage of top peak" "all peaks" } \ { "SIGMA" "NPEAKS" "PERCENT" "ALL" } } set typedef(_phaser_final_option) \ { menu { "sigma cutoff" "number of peaks" "percentage of top peak" "all peaks" } \ { "SIGMA" "NPEAKS" "PERCENT" "ALL" } } set typedef(_phaser_onoff_option) \ { menu { "on" "off" } { ON OFF } } set typedef(_phaser_refine_option) \ { menu { "refine" "fix" } { "REFINE" "FIX" } } set typedef(_phaser_set_entry_option) \ { menu { "manually" "from .sol file" } { "MANUAL" "FILE" } } set typedef(_phaser_dim_option) \ { menu { "3 dim" "5 dim" "6 dim" } { "3DIM" "5DIM" "6DIM" } } set typedef(_phaser_set_degen_option) \ { menu { "X" "Y" "Z" } { "X" "Y" "Z" } } set typedef(_phaser_set_coord_option) \ { menu { "orthogonal" "fractional" } { "ORTH" "FRACT" } } set typedef(_phaser_resolution_option) \ { menu { "dmin only" "dmin and dmax" } { "DMINONLY" "DMINMAX" } } DefineMenu _phaser_bins_option \ [list "number of bins" "width of bins" ] [list "NUMBER" "WIDTH" ] set typedef(_phaser_boxscale_option) \ { menu { "all ensembles" "selected ensemble(s)" } { "ALL" "SELECTED" } } set typedef(_phaser_clmn_option) \ { menu { "outer limit only" "inner and outer limits" } { "OUTER" "INNER_OUTER" } } DefineMenu _phaser_interpolation_option \ [list "1" "2" "3" ] [list "1" "2" "3" ] set typedef(_phaser_macrocycle_fixref) \ { menu { "fix" "refine" } { "FIX" "REFINE" } } set typedef(_laue_space_group) { varmenu LAUE_SPGP_LIST LAUE_SPGP_ALIAS 8 } return 1 } #------------------------------------------------------------------------ proc phaser_MR_run { arrayname } { #------------------------------------------------------------------------ upvar #0 $arrayname array if { $array(HKLIN_MAIN) == "" } { WarningMessage "The mtz reflection data file has not been set" return 0 } for { set n 1 } { $n <= $array(N_COMPONENT) } { incr n } { if { ($array(MW,$n) == "") && ([GetValue $arrayname MR_MODE] != "PACK") } { WarningMessage "The molecular weight for component # $n is not set" return 0 } } if { ([GetValue $arrayname MR_MODE] == "ANISOTROPY") } { return 1 } for { set n 1 } { $n <= $array(N_ENSEMBLE) } { incr n } { if { [ regexp PDB [GetValue $arrayname ENSEMBLE_OPTION,$n ] ] } { for { set p 1 } { $p <= $array(N_PDB,$n) } { incr p } { if { $array(XYZIN,[subst $n]_$p) == "" } { WarningMessage "A pdb model file for ensemble # $n has not been set" return 0 } if { $array(RMS,[subst $n]_$p) == "" } { WarningMessage "The RMS error for PDB # $p of ensemble # $n has not been set" return 0 } } } if { [ regexp MTZ [GetValue $arrayname ENSEMBLE_OPTION,$n ] ] } { if { $array(HKLIN,$n) == "" } { WarningMessage "The mtz map file for ensemble # $n has not been set" return 0 } if { $array(ENSEMBLE_PROTMW,$n) == "" } { WarningMessage "The protein molecular weight for ensemble # $n has not been set" return 0 } if { $array(ENSEMBLE_NUCLMW,$n) == "" } { WarningMessage "The nucleic acid molecular weight for ensemble # $n has not been set" return 0 } if { ($array(ENSEMBLE_EXT_X,$n) == "") || ($array(ENSEMBLE_EXT_Y,$n) == "") || ($array(ENSEMBLE_EXT_Z,$n) == "") } { WarningMessage "The extent of the model for ensemble # $n has not been (fully) defined" return 0 } if { $array(ENSEMBLE_RMS_MTZ,$n) == "" } { WarningMessage "The RMS error of the model for ensemble # $n has not been set" return 0 } if { ($array(ENSEMBLE_CEN_X,$n) == "") || ($array(ENSEMBLE_CEN_Y,$n) == "") || ($array(ENSEMBLE_CEN_Z,$n) == "") } { WarningMessage "The centre of the model for ensemble # $n has not been (fully) defined" return 0 } } } # Check for compulsory brute force rotation function AROUND search parameters if { ([GetValue $arrayname MR_MODE] == "ROTATE") && ([GetValue $arrayname MR_MODE_SELECT] == "MR_BRF") && ([GetValue $arrayname BRF_SEARCH_OPTION] == "AROUND") } { if { ($array(AROUND_ALPHA) == "") || ($array(AROUND_BETA) == "") || ($array(AROUND_GAMMA) == "") || ($array(AROUND_EULER_RANGE) == "") } { WarningMessage "The rotation function search parameters (euler angles and range) have not been (fully) defined" return 0 } } # Set up the array of input files: 1 or more mtz and maybe some pdb files set array(INPUT_FILES) "HKLIN_MAIN" for { set i 1 } { $i <= $array(N_ENSEMBLE) } { incr i } { if { [ regexp MTZ [GetValue $arrayname ENSEMBLE_OPTION,$i ] ] } { append array(INPUT_FILES) " HKLIN,$i" } if { [ regexp PDB [GetValue $arrayname ENSEMBLE_OPTION,$i ] ] } { for { set j 1 } { $j <= $array(N_PDB,$i) } { incr j } { append array(INPUT_FILES) " XYZIN,[subst $i]_$j" } } } # puts "$array(INPUT_FILES)" # The output file array is set up in phaser_MR.script set array(OUTPUT_FILES) "" # All output files with the user specified root will be saved to the project dir#set array(FILENAME_ROOT) [FileJoin [GetDefaultDirPath] $array(ROOT) ] if { ($array(MR_ROT_ENSEMBLE_ID) == "") && ([GetValue $arrayname MR_MODE] == "ROTATE") } { WarningMessage "No ensemble has been selected for the rotation search" return 0 } for { set q 1 } { $q <= $array(N_SEARCH) } { incr q } { if { ($array(MR_AUTO_ENSEMBLE_ID,$q) == "") && ([GetValue $arrayname MR_MODE] == "AUTO") } { WarningMessage "No ensemble has been selected for the molecular replacement automatic search" return 0 } } for { set n 1 } { $n <= $array(N_SEARCH) } { incr n } { if {(([lsearch -exact $array(ENSEMBLE_MENU_LIST) $array(MR_ROT_ENSEMBLE_ID)] < 0) && ([GetValue $arrayname MR_MODE] == "ROTATE")) || (([lsearch -exact $array(ENSEMBLE_MENU_LIST) $array(MR_AUTO_ENSEMBLE_ID,$n)] < 0) && ([GetValue $arrayname MR_MODE] == "AUTO")) } { WarningMessage "The ensemble specified for the mr search is not in the list of ensembles. Please select a valid ensemble before running the job." return 0 } } # Check for compulsory brute force translation function AROUND search parameters if { ([GetValue $arrayname MR_MODE] == "TRANSLATE") && ([GetValue $arrayname MR_MODE_SELECT] == "MR_BTF") && ([GetValue $arrayname BTF_SEARCH_OPTION] == "AROUND") } { if { ($array(START_X) == "") || ($array(START_Y) == "") || ($array(START_Z) == "") || ($array(AROUND_COORD_RANGE) == "") } { WarningMessage "The brute force translation function search parameters (coordinates and range) have not been (fully) defined" return 0 } } # Check for compulsory brute force translation function REGION search parameters if { ([GetValue $arrayname MR_MODE] == "TRANSLATE") && ([GetValue $arrayname MR_MODE_SELECT] == "MR_BTF") && ([GetValue $arrayname BTF_SEARCH_OPTION] == "REGION") } { if { ($array(START_X) == "") || ($array(START_Y) == "") || ($array(START_Z) == "") || ($array(END_X) == "") || ($array(END_Y) == "") || ($array(END_Z) == "") } { WarningMessage "The brute force translation function search parameters (coordinates) have not been (fully) defined" return 0 } } # Check for compulsory brute force translation function LINE search parameters if { ([GetValue $arrayname MR_MODE] == "TRANSLATE") && ([GetValue $arrayname MR_MODE_SELECT] == "MR_BTF") && ([GetValue $arrayname BTF_SEARCH_OPTION] == "LINE") } { if { ($array(START_X) == "") || ($array(START_Y) == "") || ($array(START_Z) == "") || ($array(END_X) == "") || ($array(END_Y) == "") || ($array(END_Z) == "") } { WarningMessage "The brute force translation function search parameters (coordinates) have not been (fully) defined" return 0 } } if { ( [GetValue $arrayname MR_MODE] == "TRANSLATE" ) && \ ( $array(TRA_RLIST_FILE) == "" ) } { WarningMessage "The rlist file is not set for the translation search" return 0 } if { (( [GetValue $arrayname MR_MODE] == "REFINE" ) || ( [GetValue $arrayname MR_MODE] == "RESCORE" ) ) && ( $array(SET_SOL_FILE) == "" ) } { WarningMessage "The solution .sol file is not set" return 0 } ## ([GetValue $arrayname CLMN_OUTER] < "5") if { ($array(TOG_CLMN) && !($array(CLMN_OUTER) >= 5) ) && ( ([GetValue $arrayname MR_MODE] == "ROTATE") || ([GetValue $arrayname MR_MODE] == "AUTO" ) ) } { WarningMessage "CLMN outer radius of $array(CLMN_OUTER) is set too small (Additional Parameters folder) Minimum acceptable value is 5.0 A" return 0 } # If a test space group other than mtz file one has been selected, then extract its space group number. if { ![StringSame $array(FILE_SPACEGROUP) \ [GetValue $arrayname TEST_SPACEGROUP] ] } { set array(SPACEGROUP_NUMBER) [GetSpaceGroupNumber $array(TEST_SPACEGROUP)] } else { set array(SPACEGROUP_NUMBER) "" } return 1 } #------------------------------------------------------------------------ proc phaser_MR_sg { arrayname counter_sg } { #------------------------------------------------------------------------ upvar #0 $arrayname array CreateLine line \ label "Test space group #$counter_sg" \ message "Select a test SG (same point group)\ or ALL to test all.\ NB mtz SG will NOT now be tested by default."\ widget PHASER_TEST_SG } #------------------------------------------------------------------------ proc phaser_MR_save_update { arrayname } { #------------------------------------------------------------------------ # Refers to the SAVE keyword and the various options possible upvar #0 $arrayname array if { [GetValue $arrayname SAVE_OPTION] == "SIGMA" && \ [GetValue $arrayname SAVE_CLUSTER_OPTION] == "ON" } { set array(SAVE_CLUSTER_COMB) "SIGMA_ON" } elseif { [GetValue $arrayname SAVE_OPTION] == "SIGMA" && \ [GetValue $arrayname SAVE_CLUSTER_OPTION] == "OFF" } { set array(SAVE_CLUSTER_COMB) "SIGMA_OFF" } elseif { [GetValue $arrayname SAVE_OPTION] == "NPEAKS" && \ [GetValue $arrayname SAVE_CLUSTER_OPTION] == "ON" } { set array(SAVE_CLUSTER_COMB) "NPEAKS_ON" } elseif { [GetValue $arrayname SAVE_OPTION] == "NPEAKS" && \ [GetValue $arrayname SAVE_CLUSTER_OPTION] == "OFF" } { set array(SAVE_CLUSTER_COMB) "NPEAKS_OFF" } elseif { [GetValue $arrayname SAVE_OPTION] == "PERCENT" && \ [GetValue $arrayname SAVE_CLUSTER_OPTION] == "ON" } { set array(SAVE_CLUSTER_COMB) "PERCENT_ON" } elseif { [GetValue $arrayname SAVE_OPTION] == "PERCENT" && \ [GetValue $arrayname SAVE_CLUSTER_OPTION] == "OFF" } { set array(SAVE_CLUSTER_COMB) "PERCENT_OFF" } elseif { [GetValue $arrayname SAVE_OPTION] == "ALL" && \ [GetValue $arrayname SAVE_CLUSTER_OPTION] == "ON" } { set array(SAVE_CLUSTER_COMB) "ALL_ON" } elseif { [GetValue $arrayname SAVE_OPTION] == "ALL" && \ [GetValue $arrayname SAVE_CLUSTER_OPTION] == "OFF" } { set array(SAVE_CLUSTER_COMB) "ALL_OFF" } } #------------------------------------------------------------------------ proc phaser_MR_mode_update { arrayname } { #------------------------------------------------------------------------ # Update the internal parameter MR_MODE_SELECT # This very important parameter sets the mode that phaser will run in upvar #0 $arrayname array if { [GetValue $arrayname MR_MODE] == "AUTO" } { set array(MR_MODE_SELECT) "MR_AUTO" } elseif { [GetValue $arrayname MR_MODE] == "ROTATE" && \ [GetValue $arrayname MR_MODE_ROT] == "MR_FRF" } { set array(MR_MODE_SELECT) "MR_FRF" } elseif { [GetValue $arrayname MR_MODE] == "ROTATE" && \ [GetValue $arrayname MR_MODE_ROT] == "MR_BRF" } { set array(MR_MODE_SELECT) "MR_BRF" } elseif { [GetValue $arrayname MR_MODE] == "TRANSLATE" && \ [GetValue $arrayname MR_MODE_TRAN] == "MR_FTF" } { set array(MR_MODE_SELECT) "MR_FTF" } elseif { [GetValue $arrayname MR_MODE] == "TRANSLATE" && \ [GetValue $arrayname MR_MODE_TRAN] == "MR_BTF" } { set array(MR_MODE_SELECT) "MR_BTF" } elseif { [GetValue $arrayname MR_MODE] == "REFINE" } { set array(MR_MODE_SELECT) "MR_RNP" } elseif { [GetValue $arrayname MR_MODE] == "RESCORE" } { set array(MR_MODE_SELECT) "MR_LLG" } elseif { [GetValue $arrayname MR_MODE] == "PACK" } { set array(MR_MODE_SELECT) "MR_PAK" } elseif { [GetValue $arrayname MR_MODE] == "ANISOTROPY" } { set array(MR_MODE_SELECT) "MR_ANO" } elseif { [GetValue $arrayname MR_MODE] == "CONTENT" } { set array(MR_MODE_SELECT) "MR_CCA" } phaser_MR_rescore_parameter $arrayname phaser_MR_save_update $arrayname } #------------------------------------------------------------------------ proc phaser_MR_rescore_parameter { arrayname } { #------------------------------------------------------------------------ # Update the internal parameter RESCORE_PARAMETER # This parameter keeps track of the mode of phaser selected by the user # to decide whether the RESCORE keyword is needed in the gui. # (Rescoring is only used in MR_FRF and MR_FTF and therefore AUTO) # It also monitors whether rescoring is ON/OFF in MR_FRF and MR_FTF. upvar #0 $arrayname array if { [GetValue $arrayname MR_MODE_SELECT] == "MR_FRF" && \ [GetValue $arrayname RESCORE_ONOFF] == "ON" } { set array(RESCORE_PARAMETER) "ON" set array(RESCORE_PARAMETER_ROT) "OFF" set array(RESCORE_PARAMETER_TRA) "OFF" } elseif { [GetValue $arrayname MR_MODE_SELECT] == "MR_FRF" && \ [GetValue $arrayname RESCORE_ONOFF] == "OFF" } { set array(RESCORE_PARAMETER) "OFF" set array(RESCORE_PARAMETER_ROT) "OFF" set array(RESCORE_PARAMETER_TRA) "OFF" } elseif { [GetValue $arrayname MR_MODE_SELECT] == "MR_FTF" && \ [GetValue $arrayname RESCORE_ONOFF] == "ON" } { set array(RESCORE_PARAMETER) "ON" set array(RESCORE_PARAMETER_ROT) "OFF" set array(RESCORE_PARAMETER_TRA) "OFF" } elseif { [GetValue $arrayname MR_MODE_SELECT] == "MR_FTF" && \ [GetValue $arrayname RESCORE_ONOFF] == "OFF" } { set array(RESCORE_PARAMETER) "OFF" set array(RESCORE_PARAMETER_ROT) "OFF" set array(RESCORE_PARAMETER_TRA) "OFF" } elseif { [GetValue $arrayname MR_MODE] == "AUTO" && \ [GetValue $arrayname RESCORE_ONOFF_ROT] == "ON" && \ [GetValue $arrayname RESCORE_ONOFF_TRA] == "ON" } { set array(RESCORE_PARAMETER) "OFF" set array(RESCORE_PARAMETER_ROT) "ON" set array(RESCORE_PARAMETER_TRA) "ON" } elseif { [GetValue $arrayname MR_MODE] == "AUTO" && \ [GetValue $arrayname RESCORE_ONOFF_ROT] == "ON" && \ [GetValue $arrayname RESCORE_ONOFF_TRA] == "OFF" } { set array(RESCORE_PARAMETER) "OFF" set array(RESCORE_PARAMETER_ROT) "ON" set array(RESCORE_PARAMETER_TRA) "OFF" } elseif { [GetValue $arrayname MR_MODE] == "AUTO" && \ [GetValue $arrayname RESCORE_ONOFF_ROT] == "OFF" && \ [GetValue $arrayname RESCORE_ONOFF_TRA] == "ON" } { set array(RESCORE_PARAMETER) "OFF" set array(RESCORE_PARAMETER_ROT) "OFF" set array(RESCORE_PARAMETER_TRA) "ON" } elseif { [GetValue $arrayname MR_MODE] == "AUTO" && \ [GetValue $arrayname RESCORE_ONOFF_ROT] == "OFF" && \ [GetValue $arrayname RESCORE_ONOFF_TRA] == "OFF" } { set array(RESCORE_PARAMETER) "OFF" set array(RESCORE_PARAMETER_ROT) "OFF" set array(RESCORE_PARAMETER_TRA) "OFF" } else { set array(RESCORE_PARAMETER) "NONE" } } #------------------------------------------------------------------------ proc phaser_MR_composition { arrayname counter_component } { #------------------------------------------------------------------------ # The contents of the "Composition" folder, extending frame upvar #0 $arrayname array CreateLine line \ message "Select for protein or DNA/RNA as a component of the asymmetric unit" \ label "Component #$counter_component" \ widget PROTDNA \ message "Enter the molecular weight of protein/nucleic acid #$counter_component" \ label "" \ widget COMP_OPTION -oblig \ widget MW -oblig \ message "Enter the number of copies of component #$counter_component in the asymmetric unit" \ label "Number in asymmetric unit" \ widget ASYM -oblig \ toggle_display COMP_OPTION,$counter_component open MW hide CreateLine line \ message "Select for protein or DNA/RNA as a component of the asymmetric unit" \ label "Component #$counter_component" \ widget PROTDNA \ message "Enter the file containing sequence in single letter code or fasta format" \ label "" \ widget COMP_OPTION -oblig \ message "Enter the number of copies of component #$counter_component in the asymmetric unit" \ label "Number in asymmetric unit" \ widget ASYM -oblig \ toggle_display COMP_OPTION,$counter_component open FASTA hide CreateInputFileLine line \ "Select the sequence file" "SEQ file" COMP_FILE DIR_COMP_FILE \ -toggle_display COMP_OPTION,$counter_component open FASTA hide } #------------------------------------------------------------------------ proc phaser_MR_ensemble { arrayname counter_ensemble } { #------------------------------------------------------------------------ # Sets up the main ensembles definition folder upvar #0 $arrayname array # puts "$array(ENSEMBLE_ID,$counter_ensemble)" # Set a default name for ENSEMBLE_ID of ensemb1, ensemb2, ensemb3 etc if { $array(ENSEMBLE_ID,$counter_ensemble) == "" } { set array(ENSEMBLE_ID,$counter_ensemble) "ensemble$counter_ensemble" } CreateLine line \ message "Enter unique identifier for ensemble #$counter_ensemble" \ label "Ensemble Name" widget ENSEMBLE_ID \ -command "update_phaser_MR_ensemble $arrayname" \ -oblig \ message "Define the ensemble by PDB file(s) or MTZ file" \ label "Define ensemble via" widget ENSEMBLE_OPTION \ toggle_display ENSEMBLE_OPTION,$counter_ensemble open MTZ CreateLine line \ message "Enter unique identifier for ensemble #$counter_ensemble" \ label "Ensemble Name" widget ENSEMBLE_ID \ -command "update_phaser_MR_ensemble $arrayname" \ -oblig \ message "Define the ensemble by PDB file(s) or MTZ file" \ label "Define ensemble via" widget ENSEMBLE_OPTION \ toggle_display ENSEMBLE_OPTION,$counter_ensemble open PDB OpenSubFrame frame \ -toggle_display ENSEMBLE_OPTION,$counter_ensemble open MTZ CreateInputFileLine line \ "Enter MTZ map file name (HKLIN) for ensemble # $counter_ensemble" \ "MTZ " \ HKLIN DIR_HKLIN CreateLabinLine line \ "Select calculated amplitude (FC) and calculated phase (PHIC)" \ HKLIN,$counter_ensemble "FC" FC [list FC] \ -help labin \ -sigma "PHIC" PHIC [list PHIC] CreateLine line \ message "Enter molecular weight of protein in the object\ represented by the map (from MTZ file)" \ label "Protein MW" widget ENSEMBLE_PROTMW -oblig \ message "Enter molecular weight of nucleic acid in the object\ represented by the map (from MTZ file)" \ label "Nucleic acid MW" widget ENSEMBLE_NUCLMW -oblig \ message "Enter the extent of the model in the X, Y and Z directions" \ label "Extent: X" widget ENSEMBLE_EXT_X -oblig \ label "Y" widget ENSEMBLE_EXT_Y -oblig \ label "Z" widget ENSEMBLE_EXT_Z -oblig label "Angstroms" CreateLine line \ message "Similarity to the target" \ label "RMS error" widget ENSEMBLE_RMS_MTZ -oblig \ message "Enter coordinates of the centre of the model, in Angstroms" \ label "Centre: X" widget ENSEMBLE_CEN_X -oblig \ label "Y" widget ENSEMBLE_CEN_Y -oblig \ label "Z" widget ENSEMBLE_CEN_Z -oblig label "Angstroms" CloseSubFrame # Within the Add Ensemble toggle frame, if PDB is selected for ENSEMBLE_OPTION, # then insert an extending frame for adding pdb files for each ensemble OpenSubFrame frame \ -toggle_display ENSEMBLE_OPTION,$counter_ensemble open PDB CreateExtendingFrame N_PDB phaser_MR_pdb \ "Add another PDB file to the ensemble" \ "Add superimposed PDB file to the ensemble" \ [list XYZIN DIR_XYZIN RMS_OPTION RMS ] \ -counter $counter_ensemble CloseSubFrame # Check and update the ensemble variable menu edit_phaser_MR_ensemble $arrayname $counter_ensemble } #------------------------------------------------------------------------ proc phaser_MR_search { arrayname counter_search } { #------------------------------------------------------------------------ # The auto search toggle frame code for adding extra search ensembles upvar #0 $arrayname array CreateLine line \ message "Choose an ensemble to be used for this\ molecular replacement search" \ label "Perform mr auto search using " \ widget MR_AUTO_ENSEMBLE_ID \ message "The number of copies of the ensemble to look for" \ label " Number of copies to search for" \ widget MR_AUTO_ENSEMBLE_NUM CreateExtendingFrame N_AUTO_EXTRA phaser_MR_AUTO_extra \ "Add an alternative ensemble to use in the search" \ "Add alternative ensemble to test" \ [list MR_AUTO_ENSEMBLE_ID_EXTRA] \ -counter $counter_search } #------------------------------------------------------------------------ proc phaser_MR_AUTO_extra { arrayname counter_AUTO_extra counter_search } { #------------------------------------------------------------------------ # The auto search extending frame code for adding extra ensembles to a search upvar #0 $arrayname array CreateLine line \ message "Warning: list the most likely ensemble first\ (or set PERMUTE ON via the Additional Parameters folder)"\ label " or ensemble" \ widget MR_AUTO_ENSEMBLE_ID_EXTRA } #------------------------------------------------------------------------ proc phaser_MR_frf_extra { arrayname counter } { #------------------------------------------------------------------------ # An extending frame for adding extra ensembles to a FRF search upvar #0 $arrayname array CreateLine line \ message "Select an alternative ensemble to use in this search" \ label " or ensemble" \ widget MR_FRF_ENSEMBLE_ID_EXTRA } #------------------------------------------------------------------------ proc phaser_MR_brf_extra { arrayname counter } { #------------------------------------------------------------------------ # An extending frame for adding extra ensembles to a FRF search upvar #0 $arrayname array CreateLine line \ message "Select an alternative ensemble to use in this search" \ label " or ensemble" \ widget MR_BRF_ENSEMBLE_ID_EXTRA } #------------------------------------------------------------------------ proc phaser_MR_pdb { arrayname counter_pdb counter_ensemble } { #------------------------------------------------------------------------ # The ensemble pdb extending frame lines upvar #0 $arrayname array CreateInputFileLine line \ "Select a PDB file associated with ensemble #$counter_ensemble " \ "PDB #$counter_pdb" \ XYZIN DIR_XYZIN CreateLine line \ message "Specify RMS error explicitly in Angstrom, or implicitly\ via the sequence identity (percentage or a fraction)" \ label "Similarity of PDB #$counter_pdb to the target structure" \ widget RMS_OPTION \ widget RMS -oblig } #------------------------------------------------------------------------ proc update_phaser_MR_ensemble { arrayname } { #------------------------------------------------------------------------ # This is called whenever the user clicks into the widget for an # ensemble name # It looks like an empty (redundant) procedure but is needed to ensure # that $array(N_ENSEMBLE) gets handed correctly to the menu procedure upvar #0 $arrayname array update_phaser_MR_ensemble_menu $arrayname $array(N_ENSEMBLE) } #------------------------------------------------------------------------ proc update_phaser_MR_ensemble_menu { arrayname n_ensemble } { #------------------------------------------------------------------------ # Updates the variable menu of ensembles upvar #0 $arrayname array # Build up list for menu set menu {} for { set n 1 } { $n <= $n_ensemble } { incr n } { lappend menu $array(ENSEMBLE_ID,$n) } # Do the update UpdateVariableMenu $arrayname initialise 0 ENSEMBLE_MENU_LIST $menu } #------------------------------------------------------------------------ proc edit_phaser_MR_ensemble { arrayname counter_ensemble } { #------------------------------------------------------------------------ # When an ensemble is removed or added, need to update the variable menu # for ensemble selection. # counter_ensemble is passed from the calling procedure. It is the # number of ensembles (= number of frames) upvar #0 $arrayname array set usermenu {} set alias {} # Create the ensemble menu list and its alias for { set n 1 } { $n <= $counter_ensemble } { incr n } { lappend usermenu "$n: $array(ENSEMBLE_ID,$n)" } for { set n 1 } { $n <= $counter_ensemble } { incr n } { lappend alias "$array(ENSEMBLE_ID,$n)" } # Update ENSEMBLE_ID if an ensemble is deleted and its ENSEMBLE_ID # is still set to the default ensemb$counter_ensemble # (which will now be out by one (one too high)) # regexp as below on "ensemb1" produces j1_whole=ensemb1 # j2_root=ensemb # j3_num=1 if { $counter_ensemble > 0 } { for { set p 1 } { $p <= $array(N_ENSEMBLE) } { incr p } { if { [regexp "^(ensemb)(\[0-9\])$" $array(ENSEMBLE_ID,$p) \ j1_whole j2_root j3_num] } { # If the trailing number (j3_num) is different from # the current molecule number (p) then reset the id if { $j3_num != $p } { set array(ENSEMBLE_ID,$p) "ensemb$p" } } } } # Update the variable menu with the list of ensemble names update_phaser_MR_ensemble_menu $arrayname $counter_ensemble } #------------------------------------------------------------------------ proc update_ensemble_menu { arrayname n_ensemble } { #------------------------------------------------------------------------ # Updates the variable menu of ensembles upvar #0 $arrayname array # Build list for menu set menu {} for { set n 1} {$n <= $n_ensemble } { incr n } { lappend menu $array(ENSEMBLE_ID,$n) } UpdateVariableMenu $arrayname initialise 0 ENSEMBLE_MENU_LIST $menu } #------------------------------------------------------------------------ proc phaser_MR_set_test_space_group { arrayname } { #------------------------------------------------------------------------ # To set up the choice of test space groups possible (those in the same # point group) given the space group from the mtz file upvar #0 $arrayname array set spgp_list {} set spgp_alias {} set laue_no [GetLaueGroupNumber $array(FILE_SPACEGROUP)] # laue_no is zero if FILE_SPACEGROUP is not in the standard list # update the list of spacegroups varlabel phaser_MR_updatevarlabel $arrayname FILE_SPACEGROUP if { $laue_no <= 0 } { lappend spgp_list $array(FILE_SPACEGROUP) lappend spgp_alias [GetSpaceGroupNumber $array(FILE_SPACEGROUP)] } else { set spgp_alias [GetLaueGroup $laue_no] foreach gp_no $spgp_alias { lappend spgp_list [GetSpaceGroupCode $gp_no] } } # GetLaueGroup returns a list of space groups for the given Laue Group UpdateVariableMenu $arrayname initialise [llength $array(LAUE_SPGP_LIST)] \ LAUE_SPGP_LIST $spgp_list \ MODEL_ALIAS_LIST $spgp_alias set array(PHASER_TEST_SG) [GetSpaceGroupCode $array(FILE_SPACEGROUP)] } #------------------------------------------------------------------------ proc phaser_MR_updatevarlabel { arrayname FILE_SPACEGROUP } { #------------------------------------------------------------------------ # procedure to update the FILE_SPACEGROUP varlabel upvar #0 $arrayname array set field_list [GetWidget $arrayname FILE_SPACEGROUP] foreach field $field_list { if { [winfo exists $field] } { $field configure -text $array(FILE_SPACEGROUP) } } } #------------------------------------------------------------------------ proc phaser_MR_tog_activate {arrayname} { #------------------------------------------------------------------------ upvar #0 $arrayname array if { [StringSame $array(MR_MODE_SELECT) MR_FRF] } { set array(TOG_FRF_TARGET) "1" } elseif { [StringSame $array(MR_MODE_SELECT) MR_FTF] } { set array(TOG_FTF_TARGET) "1" } else { set array(TOG_LIKELIHOOD_TARGET) "1" } } #------------------------------------------------------------------------ proc phaser_MR_set_reso {arrayname} { #------------------------------------------------------------------------ upvar #0 $arrayname array if { ( $array(RESOLUTION_DMIN) >= 2.5 ) } { set array(RESOLUTION_DMIN_MR) [GetValue $arrayname RESOLUTION_DMIN] } else { set array(RESOLUTION_DMIN_MR) 2.5 } } #------------------------------------------------------------------------ proc phaser_MR_task_window {arrayname} { #------------------------------------------------------------------------ upvar #0 $arrayname array global configure if { [CreateTaskWindow $arrayname \ "Maximum Likelihood Molecular Replacement"\ "Phaser" \ [ list "Define data (anistropy correction)" \ "Define data (cell content analysis)" \ "Define data" \ "Composition of the asymmetric unit" \ "Define ensembles (each comprising possible model(s)\ for a protein/nucleic acid component)" \ "Fast rotation function search" \ "Brute force rotation function search" \ "Fast translation function search" \ "Brute force translation function search" \ "Solution refinement" \ "Solution rescoring" \ "Solution packing" \ "Auto search (fast rotation function,\ fast translation function and packing)" \ "Define search SETs (any already known rotations/translations)" \ "Additional parameters (ensure a parameter's\ toggle button is on to activate changes made)" ] \ ] == 0 } return # SetProgramHelpFile phaser #=PROTOCOL=============================================================== OpenFolder protocol CreateTitleLine line TITLE # Sets up the central menus for choosing the mode of phaser # whether rotation, translation or refinement/rescoring searches CreateLine line \ label "Mode for molecular replacement" \ message "The central menu: select the molecular replacement\ mode for phaser to run" \ widget MR_MODE \ -command "phaser_MR_mode_update $arrayname" \ toggle_display MR_MODE open [list ANISOTROPY REFINE RESCORE PACK AUTO CONTENT ] CreateLine line \ label "Mode for molecular replacement" \ message "The central menu: select the molecular replacement\ mode for phaser to run" \ widget MR_MODE \ -command "phaser_MR_mode_update $arrayname" \ message "RF: rotation function;\ ML: maximum likelihood" \ label "using" \ widget MR_MODE_ROT \ -command "phaser_MR_mode_update $arrayname" \ toggle_display MR_MODE open ROTATE CreateLine line \ label "Mode for molecular replacement" \ message "The central menu: select the molecular replacement\ mode for phaser to run" \ widget MR_MODE \ -command "phaser_MR_mode_update $arrayname" \ message "TF: translation function;\ ML: maximum likelihood" \ label "using" \ widget MR_MODE_TRAN \ -command "phaser_MR_mode_update $arrayname" \ toggle_display MR_MODE open TRANSLATE #=FILE=================================================================== # OpenFolder file #======================================================================== # The "Define data (anistropy correction)" folder OpenFolder 1 MR_MODE open ANISOTROPY hide CreateInputFileLine line \ "Enter MTZ file name (HKLIN)" \ "MTZ in " \ HKLIN_MAIN DIR_HKLIN_MAIN \ -setfileparam resolution_min RESOLUTION_DMAX \ -setfileparam resolution_max RESOLUTION_DMIN \ -setfileparam space_group_name FILE_SPACEGROUP \ -command "phaser_MR_set_test_space_group $arrayname" CreateLabinLine line \ "Select amplitude (F) and sigma (SIGF)" \ HKLIN_MAIN "F" F [list F] \ -help labi \ -sigma "SigmaF" SIGF {} #======================================================================== # The "Define data (cell content analysis)" folder OpenFolder 2 MR_MODE open [list CONTENT ] hide CreateInputFileLine line \ "Enter MTZ file name (HKLIN)" \ "MTZ in " \ HKLIN_MAIN DIR_HKLIN_MAIN \ -setfileparam resolution_min RESOLUTION_DMAX \ -setfileparam resolution_max RESOLUTION_DMIN \ -setfileparam space_group_name FILE_SPACEGROUP \ -command "phaser_MR_set_reso $arrayname" # $line.l2 configure -width 7 -background $configure(COLOUR_BACKGROUND) CreateLabinLine line \ "Select amplitude (F) and sigma (SIGF)" \ HKLIN_MAIN "F" F {NULL} \ -sigma "SIGF" SIGF {NULL} CreateLine line \ message "Default is to take all data" \ widget TOG_RESOLUTION -toggleon \ label "Resolution range" \ message "Enter dmax, in Angstroms" \ widget RESOLUTION_DMAX \ label "A to" \ widget RESOLUTION_DMIN \ label "A" \ toggle_display MR_MODE hide PACK #======================================================================== # The "Define data" folder OpenFolder 3 MR_MODE hide [list ANISOTROPY CONTENT ] open CreateInputFileLine line \ "Enter MTZ file name (HKLIN)" \ "MTZ in " \ HKLIN_MAIN DIR_HKLIN_MAIN \ -setfileparam resolution_min RESOLUTION_DMAX \ -setfileparam resolution_max RESOLUTION_DMIN \ -setfileparam space_group_name FILE_SPACEGROUP \ -command "phaser_MR_set_test_space_group $arrayname" \ -command "phaser_MR_set_reso $arrayname" # $line.l2 configure -width 7 -background $configure(COLOUR_BACKGROUND) CreateLabinLine line \ "Select amplitude (F) and sigma (SIGF)" \ HKLIN_MAIN "F" F {NULL} \ -sigma "SIGF" SIGF {NULL} CreateLine line \ message "Default is to take all data from low resolution limit\ to the greater of dmin and 2.5 A" \ widget TOG_RESOLUTION -toggleon \ label "Resolution range" \ message "Enter dmax, in Angstroms" \ widget RESOLUTION_DMAX \ label "A to" \ message "If the dataset goes to higher than 2.5 A resolution,\ then a default dmin of 2.5 A is set." \ widget RESOLUTION_DMIN_MR \ label "A" \ toggle_display MR_MODE hide PACK OpenSubFrame frame CreateLine line \ message "Space group read from mtz file.\ By default, phaser is run with this space group" \ label "Space group read from mtz file" \ varlabel FILE_SPACEGROUP \ message "Run Phaser with a different space group" \ label "; run Phaser with space group" \ widget TEST_SPACEGROUP \ toggle_display MR_MODE open [list ROTATE REFINE RESCORE PACK] CreateLine line \ message "Space group read from mtz file." \ label "Space group read from mtz file" \ varlabel FILE_SPACEGROUP \ toggle_display MR_MODE hide [list ROTATE REFINE RESCORE PACK] CreateLine line \ message "Specify the space group(s) to run Phaser with" \ label "Run Phaser with" \ widget SPACEGROUP_OPTION \ toggle_display MR_MODE open [list AUTO TRANSLATE] CloseSubFrame OpenSubFrame frame \ -toggle_display SPACEGROUP_OPTION open SG_ALT CreateExtendingFrame N_SG phaser_MR_sg \ "Add another test space group" \ "Add another space group" \ [list PHASER_TEST_SG ] \ toggle_display MR_MODE open [list AUTO TRANSLATE] CloseSubFrame CreateLine line \ message "Default number of top pdbfiles or mtzfiles is 1" \ label "Number of top solutions to output as PDB and MTZ files"\ widget TOPFILES \ label "NB: MTZ files not output for all modes" # $line.l2 configure -width 7 -background $configure(COLOUR_BACKGROUND) #======================================================================== # The "Composition of the asymmetric unit" folder OpenFolder 4 MR_MODE hide [list PACK] open CreateExtendingFrame N_COMPONENT phaser_MR_composition \ "Define another protein or nucleic acid component" "Define another component" \ [list PROTDNA MW ASYM COMP_OPTION COMP_FILE DIR_COMP_FILE ] #======================================================================== # The "Define ensembles" folder OpenFolder 5 MR_MODE hide [list ANISOTROPY CONTENT ] open CreateToggleFrame N_ENSEMBLE phaser_MR_ensemble \ "Define another ensemble" \ "Ensemble #" \ "Add ensemble" \ [list ENSEMBLE_ID ENSEMBLE_OPTION HKLIN DIR_HKLIN LABIN FC PHIC N_PDB ] \ -edit_proc edit_phaser_MR_ensemble \ -child phaser_MR_pdb #======================================================================== # The "Fast rotation function search" folder OpenFolder 6 MR_MODE_SELECT open MR_FRF hide CreateLine line \ message "Choose an ensemble to be used for the rotation search" \ label "Perform mr rotation search using ensemble" \ widget MR_ROT_ENSEMBLE_ID CreateExtendingFrame N_FRF_EXTRA phaser_MR_frf_extra \ "Add an alternative ensemble to be searched for" \ "Add an alternative search ensemble" \ [list MR_FRF_ENSEMBLE_ID_EXTRA] CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ message "Enter the sigma value to use in the final selection process" \ widget FINAL_SIGMA \ toggle_display FINAL_OPTION open SIGMA CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ message "Enter the number of peaks to use in the final selection process" \ widget FINAL_NPEAKS \ toggle_display FINAL_OPTION open NPEAKS CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ message "Enter the percent value of the top peak to use for\ the final selection process" \ message "Enter the percentage value of the top peak to use in the\ final selection process" \ widget FINAL_PERCENT \ toggle_display FINAL_OPTION open PERCENT CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ toggle_display FINAL_OPTION open ALL #======================================================================== # The "Brute force rotation function search" folder OpenFolder 7 MR_MODE_SELECT open MR_BRF hide CreateLine line \ message "Select to perform a full or restricted search" \ label "Perform" \ widget BRF_SEARCH_OPTION \ message "Choose the ensemble to be used for molecular replacement" \ label "mr rotation search using ensemble" \ widget MR_ROT_ENSEMBLE_ID CreateExtendingFrame N_BRF_EXTRA phaser_MR_brf_extra \ "Add an alternative ensemble to be searched for" \ "Add an alternative search ensemble" \ [list MR_BRF_ENSEMBLE_ID_EXTRA] CreateLine line \ message "Restrict the search to region around this set of Euler angles" \ label "Euler angles for search: alpha" \ widget AROUND_ALPHA -oblig \ label "beta" \ widget AROUND_BETA -oblig \ label "gamma" \ widget AROUND_GAMMA -oblig \ message "Rotational distance around the given Euler angle set" \ label "with search range" \ widget AROUND_EULER_RANGE -oblig \ toggle_display BRF_SEARCH_OPTION open AROUND CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ message "Enter the sigma value to use in the final selection process" \ widget FINAL_SIGMA \ toggle_display FINAL_OPTION open SIGMA CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ message "Enter the number of peaks to use in the final selection process" \ widget FINAL_NPEAKS \ toggle_display FINAL_OPTION open NPEAKS CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ message "Enter the percent value of the top peak to use for\ the final selection process" \ message "Enter the percentage value of the top peak to use in the\ final selection process" \ widget FINAL_PERCENT \ toggle_display FINAL_OPTION open PERCENT CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ toggle_display FINAL_OPTION open ALL #======================================================================== # The "Fast translation function search" folder OpenFolder 8 MR_MODE_SELECT open MR_FTF hide CreateLine line \ message "A .rlist file is a Phaser rotation search results file" \ label "Define orientations for translation search\ and any known rotations/translations (SETs) from a .rlist file" CreateInputFileLine line \ "A .rlist file is a Phaser rotation search results file" \ ".rlist file" \ TRA_RLIST_FILE DIR_TRA_RLIST_FILE CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ message "Enter the sigma value to use in the final selection process" \ widget FINAL_SIGMA \ toggle_display FINAL_OPTION open SIGMA CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ message "Enter the number of peaks to use in the final selection process" \ widget FINAL_NPEAKS \ toggle_display FINAL_OPTION open NPEAKS CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ message "Enter the percent value of the top peak to use for\ the final selection process" \ message "Enter the percentage value of the top peak to use in the\ final selection process" \ widget FINAL_PERCENT \ toggle_display FINAL_OPTION open PERCENT CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ toggle_display FINAL_OPTION open ALL #======================================================================== # The "Brute force translation function search" folder OpenFolder 9 MR_MODE_SELECT open MR_BTF hide CreateLine line \ message "Select search type: full, around a point,\ within a region, along a line or within a plane" \ label "Perform" \ widget BTF_SEARCH_OPTION \ # message "Choose the ensemble to be used for molecular replacement" \ label "mr translation search" CreateLine line \ message "Select the coordinate system" \ label "Search around" \ widget COORD_SYS \ message "Enter the search coordinates" \ label "coordinates X" \ widget START_X -oblig \ label "Y" \ widget START_Y -oblig \ label "Z" \ widget START_Z -oblig \ message "Enter in Angstroms the range around XYZ to search" \ label "with search range" \ widget AROUND_COORD_RANGE -oblig \ toggle_display BTF_SEARCH_OPTION open AROUND CreateLine line \ message "Select the coordinate system the region is defined in" \ label "Region:" \ widget COORD_SYS \ message "Enter the start coordinates X,Y,Z for the region" \ label "coords X" \ widget START_X -oblig \ label "Y" \ widget START_Y -oblig \ label "Z" \ widget START_Z -oblig \ message "Enter the end coordinates X,Y,Z for the region" \ label "and X" \ widget END_X -oblig \ label "Y" \ widget END_Y -oblig \ label "Z" \ widget END_Z -oblig \ toggle_display BTF_SEARCH_OPTION open REGION CreateLine line \ message "Select the coordinate system the line is defined in" \ label "Line:" \ widget COORD_SYS \ message "Enter the start coordinates X,Y,Z for the line definition" \ label "coords X" \ widget START_X -oblig \ label "Y" \ widget START_Y -oblig \ label "Z" \ widget START_Z -oblig \ message "Enter the end coordinates X,Y,Z for the line definition" \ label "to X" \ widget END_X -oblig \ label "Y" \ widget END_Y -oblig \ label "Z" \ widget END_Z -oblig \ toggle_display BTF_SEARCH_OPTION open LINE CreateLine line \ message "Enter the direction X,Y,Z for the degenerate search"\ label "Search in the plane perpendicular to the direction of " \ widget DEGEN_DIR \ toggle_display BTF_SEARCH_OPTION open DEGENERATE CreateLine line \ message "A .rlist file is a Phaser rotation search results file" \ label "Define orientations for translation search\ and any known rotations/translations (SETs) from a .rlist file" CreateInputFileLine line \ "Define rotation angles for the translation search from a .rlist file\ (Phaser rotation search results file)" \ ".rlist file" \ TRA_RLIST_FILE DIR_TRA_RLIST_FILE CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ message "Enter the sigma value to use in the final selection process" \ widget FINAL_SIGMA \ toggle_display FINAL_OPTION open SIGMA CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ message "Enter the number of peaks to use in the final selection process" \ widget FINAL_NPEAKS \ toggle_display FINAL_OPTION open NPEAKS CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ message "Enter the percent value of the top peak to use for\ the final selection process" \ message "Enter the percentage value of the top peak to use in the\ final selection process" \ widget FINAL_PERCENT \ toggle_display FINAL_OPTION open PERCENT CreateLine line \ message "FINAL: the final selection criterion for peaks" \ widget TOG_FINAL -toggleon \ label "Final selection criterion for peaks" \ message "Select the criterion to be used at the final selection of peaks \ Default is PERCENT 75" \ widget FINAL_OPTION \ toggle_display FINAL_OPTION open ALL #======================================================================== # The "Solution refinement" protocol folder OpenFolder 10 MR_MODE_SELECT open MR_RNP hide CreateInputFileLine line \ "Define any known rotations/translations from a .sol file\ (Phaser search results file)" \ ".sol file" \ SET_SOL_FILE DIR_SET_SOL_FILE #======================================================================== # The "Solution rescoring" protocol folder OpenFolder 11 MR_MODE_SELECT open MR_LLG hide # CreateLine line \ message "" \ label "Rescore target function" \ widget RESCORE_TARGET_OPTION CreateInputFileLine line \ "Define any known rotations/translations from a .sol file\ (Phaser search results file)" \ ".sol file" \ SET_SOL_FILE DIR_SET_SOL_FILE #======================================================================== # The "Solution packing" protocol folder OpenFolder 12 MR_MODE_SELECT open MR_PAK hide CreateLine line \ message "Default for allowed C-alpha clashes is 0;\ increase for low-homology models" \ label "Packing tolerance: number of clashes allowed" \ widget PACK # label "Packing tolerance: number of C-alpha clashes allowed" \ CreateInputFileLine line \ "Define any known rotations/translations from a .sol file\ (Phaser search results file)" \ ".sol file" \ SET_SOL_FILE DIR_SET_SOL_FILE #======================================================================== # The "Auto search" protocol folder OpenFolder 13 MR_MODE_SELECT open MR_AUTO hide CreateToggleFrame N_SEARCH phaser_MR_search \ "Perform another mr auto search" \ "Search #" \ "Add another search" \ [list MR_AUTO_ENSEMBLE_ID \ MR_AUTO_ENSEMBLE_NUM \ MR_AUTO_ENSEMBLE_ID_EXTRA \ N_AUTO_EXTRA ] \ -child phaser_MR_AUTO_extra CreateLine line \ message "Default for allowed C-alpha clashes is 0;\ increase for low-homology models" \ widget TOG_PACK -toggleon \ label "Packing tolerance: number of clashes allowed" \ widget PACK # label "Packing tolerance: number of C-alpha clashes allowed" \ OpenSubFrame frame -toggle_display MR_MODE open [list AUTO] CreateLine line \ message "FINAL: the final selection criterion for the rotation search peaks" \ widget TOG_FINAL_ROT -toggleon \ label "Final selection criterion for ROTATION search peaks" \ message "Select the criterion to be used at the final selection of peaks\ for the rotation search. Default is PERCENT 75" \ widget FINAL_OPTION_ROT \ message "Enter the sigma value to use in the final selection process\ for the rotation search" \ widget FINAL_SIGMA_ROT \ toggle_display FINAL_OPTION_ROT open SIGMA CreateLine line \ message "FINAL: the final selection criterion for the rotation search peaks" \ widget TOG_FINAL_ROT -toggleon \ label "Final selection criterion for ROTATION search peaks" \ message "Select the criterion to be used at the final selection of peaks\ for the rotation search. Default is PERCENT 75" \ widget FINAL_OPTION_ROT \ message "Enter the number of peaks to use in the final selection process\ for the rotation search" \ widget FINAL_NPEAKS_ROT \ toggle_display FINAL_OPTION_ROT open NPEAKS CreateLine line \ message "FINAL: the final selection criterion for the rotation search peaks" \ widget TOG_FINAL_ROT -toggleon \ label "Final selection criterion for ROTATION search peaks" \ message "Select the criterion to be used at the final selection of peaks\ for the rotation search. Default is PERCENT 75" \ widget FINAL_OPTION_ROT \ message "Enter the percentage value of the top peak to use in the\ final selection process of the rotation search" \ widget FINAL_PERCENT_ROT \ toggle_display FINAL_OPTION_ROT open PERCENT CreateLine line \ message "FINAL: the final selection criterion for the rotation search peaks" \ widget TOG_FINAL_ROT -toggleon \ label "Final selection criterion for ROTATION search peaks" \ message "Select the criterion to be used at the final selection of peaks\ for the rotation search. Default is PERCENT 75" \ widget FINAL_OPTION_ROT \ toggle_display FINAL_OPTION_ROT open ALL CreateLine line \ message "FINAL: the final selection criterion for the translation search peaks" \ widget TOG_FINAL_TRA -toggleon \ label "Final selection criterion for TRANSLATION search peaks" \ message "Select the criterion to be used at the final selection of peaks\ for the transl. search. Default is PERCENT 75" \ widget FINAL_OPTION_TRA \ message "Enter the sigma value to use in the final selection process\ for the translation search" \ widget FINAL_SIGMA_TRA \ toggle_display FINAL_OPTION_TRA open SIGMA CreateLine line \ message "FINAL: the final selection criterion for the translation search peaks" \ widget TOG_FINAL_TRA -toggleon \ label "Final selection criterion for TRANSLATION search peaks" \ message "Select the criterion to be used at the final selection of peaks\ for the transl. search. Default is PERCENT 75" \ widget FINAL_OPTION_TRA \ message "Enter the number of peaks to use in the final selection process\ for the translation search" \ widget FINAL_NPEAKS_TRA \ toggle_display FINAL_OPTION_TRA open NPEAKS CreateLine line \ message "FINAL: the final selection criterion for the translation search peaks" \ widget TOG_FINAL_TRA -toggleon \ label "Final selection criterion for TRANSLATION search peaks" \ message "Select the criterion to be used at the final selection of peaks\ for the transl. search. Default is PERCENT 75" \ widget FINAL_OPTION_TRA \ message "Enter the percentage value of the top peak to use in the\ final selection process of the translation search" \ widget FINAL_PERCENT_TRA \ toggle_display FINAL_OPTION_TRA open PERCENT CreateLine line \ message "FINAL: the final selection criterion for the translation search peaks" \ widget TOG_FINAL_TRA -toggleon \ label "Final selection criterion for TRANSLATION search peaks" \ message "Select the criterion to be used at the final selection of peaks\ for the transl. search. Default is PERCENT 75" \ widget FINAL_OPTION_TRA \ toggle_display FINAL_OPTION_TRA open ALL CloseSubFrame #======================================================================== # The "Define search SETs" folder OpenFolder 14 MR_MODE closed [list AUTO ROTATE] hide CreateInputFileLine line \ "Define any known rotations/translations from a .sol file\ (Phaser search results file). This is optional." \ ".sol file" \ SET_SOL_FILE DIR_SET_SOL_FILE #======================================================================== # The "Additional parameters" folder # Miscellaneous options which most users will not need to change OpenFolder 15 MR_MODE closed OpenSubFrame frame -toggle_display MR_MODE open AUTO hide CreateLine line \ label "" CreateLine line \ label "Criteria for the rotation search" -italic \ CreateLine line \ message "SAVE: criterion for selecting the highest peaks to be saved.\ Default is PERCENT 75" \ widget TOG_SAVE_SELECT_ROT -toggleon \ label "Save peak criterion" \ widget SAVE_OPTION_ROT \ -command "phaser_MR_save_update $arrayname" \ message "Enter the sigma cutoff value" \ widget SAVE_SIGMA_ROT \ toggle_display SAVE_OPTION_ROT open SIGMA CreateLine line \ message "SAVE: criterion for selecting the highest peaks to be saved.\ Default is PERCENT 75" \ widget TOG_SAVE_SELECT_ROT -toggleon \ label "Save peak criterion" \ message "Default is PERCENT 75" \ widget SAVE_OPTION_ROT \ -command "phaser_MR_save_update $arrayname" \ message "Enter the number of top peaks to save" \ widget SAVE_NPEAKS_ROT \ toggle_display SAVE_OPTION_ROT open NPEAKS CreateLine line \ message "SAVE: criterion for selecting the highest peaks to be saved.\ Default is PERCENT 75" \ widget TOG_SAVE_SELECT_ROT -toggleon \ label "Save peak criterion" \ message "Default is PERCENT 75" \ widget SAVE_OPTION_ROT \ -command "phaser_MR_save_update $arrayname" \ message "Peaks above this percentage of the top are saved" \ widget SAVE_PERCENT_ROT \ toggle_display SAVE_OPTION_ROT open PERCENT CreateLine line \ message "SAVE: criterion for selecting the highest peaks to be saved.\ Default is PERCENT 75" \ widget TOG_SAVE_SELECT_ROT -toggleon \ label "Save peak criterion" \ message "Default is PERCENT 75" \ widget SAVE_OPTION_ROT \ -command "phaser_MR_save_update $arrayname" \ toggle_display SAVE_OPTION_ROT open ALL CreateLine line \ message "SAVE: specify clustering to be on or off" \ widget TOG_SAVE_CLUSTER_ROT -toggleon \ label "Save: clustering" \ message "Select whether raw or clustered peaks are to be saved" \ widget SAVE_CLUSTER_OPTION_ROT \ -command "phaser_MR_save_update $arrayname" \ message "With clustered peaks, NDUMP raw peaks will be dumped\ to the output" \ label "Dump" \ widget SAVE_NDUMP_ROT \ toggle_display SAVE_CLUSTER_OPTION_ROT open ON hide CreateLine line \ message "SAVE: specify clustering to be on or off" \ widget TOG_SAVE_CLUSTER_ROT -toggleon \ label "Save: clustering" \ message "Select whether raw or clustered peaks are to be saved" \ widget SAVE_CLUSTER_OPTION_ROT \ -command "phaser_MR_save_update $arrayname" \ message "If not saving clustered peaks, clustering can still be performed\ with the results logged to the log file" \ label "Log" \ widget SAVE_LOG_OPTION_ROT \ toggle_display SAVE_CLUSTER_OPTION_ROT open OFF hide CreateLine line \ message "RESCORE: select whether or not to apply rescoring\ (rescoring parameters continued on line below)" \ widget TOG_RESCORE_ROT -toggleon \ label "Rescoring" \ widget RESCORE_ONOFF_ROT \ -command "phaser_MR_rescore_parameter $arrayname" \ toggle_display RESCORE_PARAMETER_ROT open OFF # CreateLine line \ label "" \ toggle_display RESCORE_PARAMETER_ROT open OFF CloseSubFrame OpenSubFrame frame -toggle_display RESCORE_PARAMETER_ROT open ON hide CreateLine line \ message "RESCORE: select whether or not to apply rescoring\ (rescoring parameters continued on line below)" \ widget TOG_RESCORE_ROT -toggleon \ label "Rescoring" \ widget RESCORE_ONOFF_ROT \ -command "phaser_MR_rescore_parameter $arrayname" CreateLine line \ message "RESCORE: select the criterion for rescoring peaks."\ widget TOG_RESCORE_SELECT_ROT -toggleon \ label "Rescore criterion" \ widget RESCORE_OPTION_ROT \ message "Enter the sigma cutoff value for rescoring" \ widget RESCORE_SIGMA_ROT \ toggle_display RESCORE_OPTION_ROT open SIGMA CreateLine line \ message "RESCORE: select the criterion for rescoring peaks."\ widget TOG_RESCORE_SELECT_ROT -toggleon \ label "Rescore criterion" \ widget RESCORE_OPTION_ROT \ message "Enter the number of peaks for rescoring" \ widget RESCORE_NPEAKS_ROT \ toggle_display RESCORE_OPTION_ROT open NPEAKS CreateLine line \ message "RESCORE: select the criterion for rescoring peaks."\ widget TOG_RESCORE_SELECT_ROT -toggleon \ label "Rescore criterion" \ widget RESCORE_OPTION_ROT \ message "Enter the percent value of the top peak to use for rescoring" \ widget RESCORE_PERCENT_ROT \ toggle_display RESCORE_OPTION_ROT open PERCENT CreateLine line \ message "RESCORE: select the criterion for rescoring peaks."\ widget TOG_RESCORE_SELECT_ROT -toggleon \ label "Rescore criterion" \ widget RESCORE_OPTION_ROT \ toggle_display RESCORE_OPTION_ROT open ALL CreateLine line \ message "RESCORE: select whether raw or clustered peaks are to be used\ in the rescoring" \ widget TOG_RESCORE_CLUSTER_ROT -toggleon \ label "Rescore clustering" \ widget RESCORE_CLUSTER_OPTION_ROT \ message "With clustered peaks, NDUMP raw peaks will be dumped\ to the output" \ label "Dump" \ widget RESCORE_NDUMP_ROT \ toggle_display RESCORE_CLUSTER_OPTION_ROT open ON CreateLine line \ message "RESCORE: select whether clustered or raw peaks are to be used\ in the rescoring" \ widget TOG_RESCORE_CLUSTER_ROT -toggleon \ label "Rescore clustering" \ widget RESCORE_CLUSTER_OPTION_ROT \ message "With clustering off, clustering may still be performed with\ the results logged to the log file" \ label "Log" \ widget RESCORE_LOG_OPTION_ROT \ toggle_display RESCORE_CLUSTER_OPTION_ROT open OFF CloseSubFrame OpenSubFrame frame -toggle_display MR_MODE open AUTO hide CreateLine line \ label "" CreateLine line \ label "Criteria for the translation search" -italic \ CreateLine line \ message "SAVE: criterion for selecting the highest peaks to be saved.\ Default is PERCENT 75" \ widget TOG_SAVE_SELECT_TRA -toggleon \ label "Save peak criterion" \ widget SAVE_OPTION_TRA \ -command "phaser_MR_save_update $arrayname" \ message "Enter the sigma cutoff value" \ widget SAVE_SIGMA_TRA \ toggle_display SAVE_OPTION_TRA open SIGMA CreateLine line \ message "SAVE: criterion for selecting the highest peaks to be saved.\ Default is PERCENT 75" \ widget TOG_SAVE_SELECT_TRA -toggleon \ label "Save peak criterion" \ message "Default is PERCENT 75" \ widget SAVE_OPTION_TRA \ -command "phaser_MR_save_update $arrayname" \ message "Enter the number of top peaks to save" \ widget SAVE_NPEAKS_TRA \ toggle_display SAVE_OPTION_TRA open NPEAKS CreateLine line \ message "SAVE: criterion for selecting the highest peaks to be saved.\ Default is PERCENT 75" \ widget TOG_SAVE_SELECT_TRA -toggleon \ label "Save peak criterion" \ message "Default is PERCENT 75" \ widget SAVE_OPTION_TRA \ -command "phaser_MR_save_update $arrayname" \ message "Peaks above this percentage of the top are saved" \ widget SAVE_PERCENT_TRA \ toggle_display SAVE_OPTION_TRA open PERCENT CreateLine line \ message "SAVE: criterion for selecting the highest peaks to be saved.\ Default is PERCENT 75" \ widget TOG_SAVE_SELECT_TRA -toggleon \ label "Save peak criterion" \ message "Default is PERCENT 75" \ widget SAVE_OPTION_TRA \ -command "phaser_MR_save_update $arrayname" \ toggle_display SAVE_OPTION_TRA open ALL CreateLine line \ message "SAVE: specify clustering to be on or off" \ widget TOG_SAVE_CLUSTER_TRA -toggleon \ label "Save: clustering" \ message "Select whether raw or clustered peaks are to be saved" \ widget SAVE_CLUSTER_OPTION_TRA \ -command "phaser_MR_save_update $arrayname" \ message "With clustered peaks, NDUMP raw peaks will be dumped\ to the output" \ label "Dump" \ widget SAVE_NDUMP_TRA \ toggle_display SAVE_CLUSTER_OPTION_TRA open ON hide CreateLine line \ message "SAVE: specify clustering to be on or off" \ widget TOG_SAVE_CLUSTER_TRA -toggleon \ label "Save: clustering" \ message "Select whether raw or clustered peaks are to be saved" \ widget SAVE_CLUSTER_OPTION_TRA \ -command "phaser_MR_save_update $arrayname" \ message "If not saving clustered peaks, clustering can still be performed\ with the results logged to the log file" \ label "Log" \ widget SAVE_LOG_OPTION_TRA \ toggle_display SAVE_CLUSTER_OPTION_TRA open OFF hide CreateLine line \ message "RESCORE: select whether or not to apply rescoring\ (rescoring parameters continued on line below)" \ widget TOG_RESCORE_TRA -toggleon \ label "Rescoring" \ widget RESCORE_ONOFF_TRA \ -command "phaser_MR_rescore_parameter $arrayname" \ toggle_display RESCORE_PARAMETER_TRA open OFF CreateLine line \ label "" \ toggle_display RESCORE_PARAMETER_TRA open OFF CloseSubFrame OpenSubFrame frame -toggle_display RESCORE_PARAMETER_TRA open ON hide CreateLine line \ message "RESCORE: select whether or not to apply rescoring\ (rescoring parameters continued on line below)" \ widget TOG_RESCORE_TRA -toggleon \ label "Rescoring" \ widget RESCORE_ONOFF_TRA \ -command "phaser_MR_rescore_parameter $arrayname" CreateLine line \ message "RESCORE: select the criterion for rescoring peaks."\ widget TOG_RESCORE_SELECT_TRA -toggleon \ label "Rescore criterion" \ widget RESCORE_OPTION_TRA \ message "Enter the sigma cutoff value for rescoring" \ widget RESCORE_SIGMA_TRA \ toggle_display RESCORE_OPTION_TRA open SIGMA CreateLine line \ message "RESCORE: select the criterion for rescoring peaks."\ widget TOG_RESCORE_SELECT_TRA -toggleon \ label "Rescore criterion" \ widget RESCORE_OPTION_TRA \ message "Enter the number of peaks for rescoring" \ widget RESCORE_NPEAKS_TRA \ toggle_display RESCORE_OPTION_TRA open NPEAKS CreateLine line \ message "RESCORE: select the criterion for rescoring peaks."\ widget TOG_RESCORE_SELECT_TRA -toggleon \ label "Rescore criterion" \ widget RESCORE_OPTION_TRA \ message "Enter the percent value of the top peak to use for rescoring" \ widget RESCORE_PERCENT_TRA \ toggle_display RESCORE_OPTION_TRA open PERCENT CreateLine line \ message "RESCORE: select the criterion for rescoring peaks."\ widget TOG_RESCORE_SELECT_TRA -toggleon \ label "Rescore criterion" \ widget RESCORE_OPTION_TRA \ toggle_display RESCORE_OPTION_TRA open ALL CreateLine line \ message "RESCORE: select whether raw or clustered peaks are to be used\ in the rescoring" \ widget TOG_RESCORE_CLUSTER_TRA -toggleon \ label "Rescore clustering" \ widget RESCORE_CLUSTER_OPTION_TRA \ message "With clustered peaks, NDUMP raw peaks will be dumped\ to the output" \ label "Dump" \ widget RESCORE_NDUMP_TRA \ toggle_display RESCORE_CLUSTER_OPTION_TRA open ON CreateLine line \ message "RESCORE: select whether clustered or raw peaks are to be used\ in the rescoring" \ widget TOG_RESCORE_CLUSTER_TRA -toggleon \ label "Rescore clustering" \ widget RESCORE_CLUSTER_OPTION_TRA \ message "With clustering off, clustering may still be performed with\ the results logged to the log file" \ label "Log" \ widget RESCORE_LOG_OPTION_TRA \ toggle_display RESCORE_CLUSTER_OPTION_TRA open OFF CreateLine line \ label "" CloseSubFrame OpenSubFrame frame -toggle_display MR_MODE_SELECT open [list MR_FRF MR_FTF] hide CreateLine line \ label "" CreateLine line \ message "SAVE: criterion for selecting the highest peaks to be saved.\ Default is PERCENT 75" \ widget TOG_SAVE_SELECT -toggleon \ label "Save peak criterion" \ widget SAVE_OPTION \ -command "phaser_MR_save_update $arrayname" \ message "Enter the sigma cutoff value" \ widget SAVE_SIGMA \ toggle_display SAVE_OPTION open SIGMA CreateLine line \ message "SAVE: criterion for selecting the highest peaks to be saved.\ Default is PERCENT 75" \ widget TOG_SAVE_SELECT -toggleon \ label "Save peak criterion" \ message "Default is PERCENT 75" \ widget SAVE_OPTION \ -command "phaser_MR_save_update $arrayname" \ message "Enter the number of top peaks to save" \ widget SAVE_NPEAKS \ toggle_display SAVE_OPTION open NPEAKS CreateLine line \ message "SAVE: criterion for selecting the highest peaks to be saved.\ Default is PERCENT 75" \ widget TOG_SAVE_SELECT -toggleon \ label "Save peak criterion" \ message "Default is PERCENT 75" \ widget SAVE_OPTION \ -command "phaser_MR_save_update $arrayname" \ message "Peaks above this percentage of the top are saved" \ widget SAVE_PERCENT \ toggle_display SAVE_OPTION open PERCENT CreateLine line \ message "SAVE: criterion for selecting the highest peaks to be saved.\ Default is PERCENT 75" \ widget TOG_SAVE_SELECT -toggleon \ label "Save peak criterion" \ message "Default is PERCENT 75" \ widget SAVE_OPTION \ -command "phaser_MR_save_update $arrayname" \ toggle_display SAVE_OPTION open ALL CreateLine line \ message "SAVE: specify clustering to be on or off" \ widget TOG_SAVE_CLUSTER -toggleon \ label "Save: clustering" \ message "Select whether raw or clustered peaks are to be saved" \ widget SAVE_CLUSTER_OPTION \ -command "phaser_MR_save_update $arrayname" \ message "With clustered peaks, NDUMP raw peaks will be dumped\ to the output" \ label "Dump" \ widget SAVE_NDUMP \ toggle_display SAVE_CLUSTER_OPTION open ON hide CreateLine line \ message "SAVE: specify clustering to be on or off" \ widget TOG_SAVE_CLUSTER -toggleon \ label "Save: clustering" \ message "Select whether raw or clustered peaks are to be saved" \ widget SAVE_CLUSTER_OPTION \ -command "phaser_MR_save_update $arrayname" \ message "If not saving clustered peaks, clustering can still be performed\ with the results logged to the log file" \ label "Log" \ widget SAVE_LOG_OPTION \ toggle_display SAVE_CLUSTER_OPTION open OFF hide CreateLine line \ message "RESCORE: select whether or not to apply rescoring\ (rescoring parameters continued on line below)" \ widget TOG_RESCORE -toggleon \ label "Rescoring" \ widget RESCORE_ONOFF \ -command "phaser_MR_rescore_parameter $arrayname" \ toggle_display RESCORE_ONOFF open OFF CreateLine line \ label "" \ toggle_display RESCORE_ONOFF open OFF CloseSubFrame OpenSubFrame frame -toggle_display RESCORE_PARAMETER open ON hide CreateLine line \ message "RESCORE: select whether or not to apply rescoring\ (rescoring parameters continued on line below)" \ widget TOG_RESCORE -toggleon \ label "Rescoring" \ widget RESCORE_ONOFF \ -command "phaser_MR_rescore_parameter $arrayname" CreateLine line \ message "RESCORE: select the criterion for rescoring peaks."\ widget TOG_RESCORE_SELECT -toggleon \ label "Rescore criterion" \ widget RESCORE_OPTION \ message "Enter the sigma cutoff value for rescoring" \ widget RESCORE_SIGMA \ toggle_display RESCORE_OPTION open SIGMA CreateLine line \ message "RESCORE: select the criterion for rescoring peaks."\ widget TOG_RESCORE_SELECT -toggleon \ label "Rescore criterion" \ widget RESCORE_OPTION \ message "Enter the number of peaks for rescoring" \ widget RESCORE_NPEAKS \ toggle_display RESCORE_OPTION open NPEAKS CreateLine line \ message "RESCORE: select the criterion for rescoring peaks."\ widget TOG_RESCORE_SELECT -toggleon \ label "Rescore criterion" \ widget RESCORE_OPTION \ message "Enter the percent value of the top peak to use for rescoring" \ widget RESCORE_PERCENT \ toggle_display RESCORE_OPTION open PERCENT CreateLine line \ message "RESCORE: select the criterion for rescoring peaks."\ widget TOG_RESCORE_SELECT -toggleon \ label "Rescore criterion" \ widget RESCORE_OPTION \ toggle_display RESCORE_OPTION open ALL CreateLine line \ message "RESCORE: select whether raw or clustered peaks are to be used\ in the rescoring" \ widget TOG_RESCORE_CLUSTER -toggleon \ label "Rescore clustering" \ widget RESCORE_CLUSTER_OPTION \ message "With clustered peaks, NDUMP raw peaks will be dumped\ to the output" \ label "Dump" \ widget RESCORE_NDUMP \ toggle_display RESCORE_CLUSTER_OPTION open ON CreateLine line \ message "RESCORE: select whether clustered or raw peaks are to be used\ in the rescoring" \ widget TOG_RESCORE_CLUSTER -toggleon \ label "Rescore clustering" \ widget RESCORE_CLUSTER_OPTION \ message "With clustering off, clustering may still be performed with\ the results logged to the log file" \ label "Log" \ widget RESCORE_LOG_OPTION \ toggle_display RESCORE_CLUSTER_OPTION open OFF CreateLine line \ label "" CloseSubFrame CreateLine line \ message "Default is to apply an anisotropy correction" \ widget TOG_ANISO \ label "Perform anisotropy correction" \ toggle_display MR_MODE hide [list CONTENT PACK] CreateLine line \ message "Controls output of PDB files containing potential solutions.\ Default depends on mode." \ widget TOG_XYZOUT -toggleon \ label "XYZ (PDB) file output" \ widget XYZOUT_ONOFF \ toggle_display MR_MODE hide [list CONTENT] CreateLine line \ message "Controls output of MTZ files with phase information from solutions.\ Default depends on mode." \ widget TOG_HKLOUT -toggleon \ label "HKL (MTZ) file output" \ widget HKLOUT_ONOFF \ toggle_display MR_MODE hide [list CONTENT PACK] CreateLine line \ message "TARGET: select the rotation target function to be used" \ widget TOG_FRF_TARGET \ label "Rotation target function" \ widget FRF_TARGET_OPTION \ -command "phaser_MR_tog_activate $arrayname" \ toggle_display MR_MODE_SELECT open [list MR_FRF MR_AUTO] hide CreateLine line \ message "TARGET: select the translation target function to be used" \ widget TOG_FTF_TARGET \ label "Translation target function" \ widget FTF_TARGET_OPTION \ -command "phaser_MR_tog_activate $arrayname" \ toggle_display MR_MODE_SELECT open [list MR_FTF MR_AUTO] hide OpenSubFrame frame -toggle_display MR_MODE hide [list PACK CONTENT] CreateLine line \ message "BINS: specify how the binning to all reflections will apply"\ widget TOG_BINS -toggleon \ label "Binning of data" \ message "BINS: specify binning by the number or width of bins" \ widget BINS_OPTION \ message "Default number is the number of reflections divided by 1000\ subject to a minimum of 6 bins" \ widget BINS_N \ message "Binning function: AS^3 + BS^2 + CS\ where S=1/reso.\ A,B,C must all be +ve and A=B=0 or A=0 or B=0"\ label "Coeffs for binning fn: A" \ widget BINS_A \ label "B" \ widget BINS_B \ label "C" \ widget BINS_C \ toggle_display BINS_OPTION open NUMBER hide CreateLine line \ message "BINS: specify how the binning to all reflections will apply"\ widget TOG_BINS -toggleon \ label "Binning of data" \ message "BINS: specify binning by the number or width of bins" \ widget BINS_OPTION \ message "Default width is 1000 reflections" \ widget BINS_W \ message "Binning function: AS^3 + BS^2 + CS\ where S=1/reso.\ A,B,C must all be +ve and A=B=0 or A=0 or B=0"\ label "Coeffs for binning fn: A" \ widget BINS_A \ label "B" \ widget BINS_B \ label "C" \ widget BINS_C \ toggle_display BINS_OPTION open WIDTH hide CreateLine line \ message "BOXSCALE: specify how finely the ensemble structure factors\ are sampled in reciprocal space" \ widget TOG_BOXSCALE -toggleon \ label "Box scale factor" \ message "The ensemble 'cell' is *(extent of molecule).\ The default value of BOXSCALE is 4" \ widget BOXSCALE CloseSubFrame OpenSubFrame frame -toggle_display MR_MODE_SELECT open [list MR_FRF MR_AUTO] hide CreateLine line \ message "CLMN: radius for decomposition of the Patterson" \ widget TOG_CLMN -toggleon \ label "CLMN sphere outer radius " \ message "Specify outer radius in Angstroms. Min acceptable value is 5 A" \ widget CLMN_OUTER CloseSubFrame OpenSubFrame frame -toggle_display MR_MODE hide [list PACK CONTENT] CreateLine line \ message "OUTLIER: choose whether to reject large, unlikely E-values" \ widget TOG_OUTLIER -toggleon \ label "Outlier rejection" \ widget OUTLIER_OPTION \ label "outlier probability" \ message "Enter cutoff probability, where outliers with a probability\ less than the cutoff are rejected" \ widget OUTLIER_PROB \ toggle_display OUTLIER_OPTION open ON CreateLine line \ message "OUTLIER: choose whether to reject large, unlikely E-values.\ Default is ON with probability 0.00001" \ widget TOG_OUTLIER -toggleon \ label "Outlier rejection" \ widget OUTLIER_OPTION \ toggle_display OUTLIER_OPTION open OFF CloseSubFrame CreateLine line \ message "Choose whether to permute the order of the search set.\ Default is OFF." \ widget TOG_PERMUTATIONS -toggleon \ label "Permute search set" \ widget PERMUTATIONS_ONOFF \ toggle_display MR_MODE open [list AUTO] CreateLine line \ message "SAMPLING: sampling of search space" \ widget TOG_SAMPLING -toggleon \ label "Sampling for rotation search" \ message "Sampling for rotation search given in degrees" \ widget SAMPLING_ROT \ toggle_display MR_MODE open ROTATE CreateLine line \ message "SAMPLING: sampling of search space" \ widget TOG_SAMPLING -toggleon \ label "Sampling for translation search" \ message "Sampling for translation search given in Angstroms" \ widget SAMPLING_TRA \ toggle_display MR_MODE open TRANSLATE CreateLine line \ message "SAMPLING: sampling of search space" \ widget TOG_SAMPLING -toggleon \ label "Sampling for rotation search" \ message "Sampling for rotation search given in degrees" \ widget SAMPLING_ROT \ label "Sampling for translation search" \ message "Sampling for translation search given in Angstroms" \ widget SAMPLING_TRA \ toggle_display MR_MODE open AUTO CreateLine line \ message "SHANNON: specify the Shannon rate for sampling the\ ensemble coordinate maps" \ widget TOG_SHANNON -toggleon \ label "Shannon factor" \ message "Shannon sampling given by (2*SHARAT). Default value is 1.5.\ Increase SHARAT to 2 to sharpen the sampling" \ widget SHANNON \ toggle_display MR_MODE hide [list PACK CONTENT] CreateLine line \ message "VERBOSE: more information included in log file than by default" \ widget TOG_VERBOSE \ label "Verbose output to log file" \ message "Verbose extra option: even more information included in log file" \ widget TOG_VERBOSE_EXTRA \ label "extra" # $line.l2 configure -width 7 -background $configure(COLOUR_BACKGROUND) }