# ======================================================================= # phaser_MR.tcl -- # # Maximum Likelihood Molecular Replacement # # CCP4Interface # # ======================================================================= #------------------------------------------------------------------------------ proc phaser_MR_prereq { } { #------------------------------------------------------------------------------ if { ![file exists [FindExecutable phaser]] } { return 0 } return 1 } #------------------------------------------------------------------------ proc phaser_MR_setup { typedefVar arrayname } { #------------------------------------------------------------------------ upvar #0 $typedefVar typedef upvar #0 $arrayname array DefineMenu _mode_menu [list "automated search" \ "rotation search" \ "translation search" \ "packing" \ "refinement and phasing" ] \ [list "AUTO" \ "ROT" \ "TRA" \ "PAK" \ "RNP" ] #for backwards compatibility DefineMenu _mode_rot \ [list "fast rotation function" "brute rotation function" ] [list "MR_FRF" "MR_BRF"] #for backwards compatibility DefineMenu _mode_tran \ [list "fast translation function" "brute translation function" ] [list "MR_FTF" "MR_BTF" ] DefineMenu _spacegroup_option \ [list "mtz space group" "mtz space group and enantiomorph" "all alternative space groups" "alternative spacegroups (listed)"] \ [list "SG_MTZ" "SG_ENANT" "SG_ALL" "SG_ALT" ] set typedef(_laue_space_group) { varmenu LAUE_SPGP_LIST LAUE_SPGP_ALIAS 8 } DefineMenu _composition_option \ [ list "average solvent content for protein crystal" "solvent content of protein crystal" "components in asymmetric unit" "fraction scattering by ensemble"] \ [ list "AVERAGE" "SOLVENT" "COMPONENT" "FRAC"] DefineMenu _protnucleic \ [list "protein" "nucleic acid" ] [list "PROTEIN" "NUCLEIC" ] DefineMenu _rmsid_option \ [list "rms difference" "sequence identity" "from pdb REMARK" "high rms from id" "low rms from id"] [list "RMS" "IDENT" "CARD" "IDHI" "IDLO"] set typedef(_mwseqnres_option) \ { menu { "molecular weight" "sequence file" "number of residues"} { "MW" "FASTA" "NRES"} } DefineMenu _ensemble_option \ [list "pdb file(s)" "map (mtz file)" ] [list "PDB" "MAP"] DefineMenu _search_type \ [list "on" "off" ] [list "SEARCH_OR" "SEARCH_SIMPLE"] DefineMenu _search_method \ [list "full" "fast" ] [list "FULL" "FAST" ] DefineMenu _brf_search_option \ [list "all angles" "around an angle" ] [list "FULL" "AROUND" ] DefineMenu _btf_search_option \ [list "full" "around" "region" "line"] [list "FULL" "AROUND" "REGION" "LINE"] DefineMenu _packing_option \ [list "best packing (up to percent)" "best packing (up to number)" "max number of clashes" "accept all solutions" ] \ [list "PERCENT" "BEST" "ALLOWED" "ALL"] set typedef(_ensemble_menu) \ { varmenu ENSEMBLE_MENU_LIST ENSEMBLE_MENU_ALIAS 15 } set typedef(_frf_target_option) \ { menu { "Fast" "Brute"} { "FAST" "BRUTE"} } set typedef(_ftf_target_option) \ { menu { "Fast" "Brute" "Phased"} { "FAST" "BRUTE" "PHASED"} } set typedef(_frf_target_type_option) \ { menu { "lert1" "correlation"} { "LERF1" "CORRELATION"} } set typedef(_ftf_target_type_option) \ { menu { "letf1" "letf2"} { "LETF1" "LETF2"} } set typedef(_peaks_option) \ { menu { "percentage of top peak" "sigma (Z-score) cutoff" "number of peaks" "all peaks"} \ { "PERCENT" "SIGMA" "NUMBER" "ALL" } } set typedef(_macro_protocol) \ { menu { "default" "custom" "fix all" "refine all"} { "DEFAULT" "CUSTOM" "OFF" "ALL"} } set typedef(_onoff) \ { menu { "on" "off" } { ON OFF } } set typedef(_tribool) \ { menu { "on" "off" "auto" } { ON OFF NOT_SET } } set typedef(_coord_option) \ { menu { "orthogonal" "fractional" } { "ORTH" "FRAC" } } return 1 } #------------------------------------------------------------------------ proc phaser_MR_run { arrayname } { #------------------------------------------------------------------------ upvar #0 $arrayname array # 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(HKLIN_MAIN) == "" } { WarningMessage "NOT SET: mtz reflection data file" return 0 } if { ([GetValue $arrayname SCATTERING] == "COMPONENT") } { for { set n 1 } { $n <= $array(N_COMPONENT) } { incr n } { if { $array(COMP_OPTION,$n) == "sequence file" && $array(COMP_FILE,$n) == "" } { WarningMessage "NOT SET: sequence file for component # $n" return 0 } if { $array(COMP_OPTION,$n) == "molecular weight" && $array(MW,$n) == "" } { WarningMessage "NOT SET: molecular weight for component # $n" return 0 } } } if { ([GetValue $arrayname SCATTERING] == "NRES")} { if { ([GetValue $arrayname COMP_NRES] == "")} { WarningMessage "NOT SET: number of residues in the composition" return 0 } } if { ([GetValue $arrayname SCATTERING] == "SOLVENT")} { if { ([GetValue $arrayname SCATTERING_SOLVENT] == "")} { WarningMessage "NOT SET: solvent content in the composition" return 0 } } 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 "NOT SET: pdb file for ensemble # $n" return 0 } if { $array(RMS_OPTION,[subst $n]_$p) != "from pdb REMARK" } { if { $array(RMS,[subst $n]_$p) == "" } { WarningMessage "NOT SET: RMS error for PDB # $p of ensemble # $n" return 0 } } } } if { [ regexp MAP [GetValue $arrayname ENSEMBLE_OPTION,$n ] ] } { if { $array(HKLIN,$n) == "" } { WarningMessage "NOT SET: mtz map file for ensemble # $n" return 0 } if { $array(ENSEMBLE_PROTMW,$n) == "" } { WarningMessage "NOT SET: protein molecular weight for ensemble # $n" return 0 } if { $array(ENSEMBLE_NUCLMW,$n) == "" } { WarningMessage "NOT SET: nucleic acid molecular weight for ensemble # $n" return 0 } if { ($array(ENSEMBLE_EXT_X,$n) == "") || ($array(ENSEMBLE_EXT_Y,$n) == "") || ($array(ENSEMBLE_EXT_Z,$n) == "") } { WarningMessage "NOT SET: extent of the model for ensemble # $n" return 0 } if { $array(ENSEMBLE_RMS_MTZ,$n) == "" } { WarningMessage "NOT SET: RMS error of the model for ensemble # $n" return 0 } if { ($array(ENSEMBLE_CEN_X,$n) == "") || ($array(ENSEMBLE_CEN_Y,$n) == "") || ($array(ENSEMBLE_CEN_Z,$n) == "") } { WarningMessage "NOT SET: centre of the model for ensemble # $n" return 0 } } } # Check for compulsory brute force rotation function AROUND search parameters if { ([GetValue $arrayname MR_MODE] == "ROT") && ([GetValue $arrayname FRF_TARGET_OPTION] == "BRUTE") && ([GetValue $arrayname BRF_SEARCH_OPTION] == "AROUND") } { if { ($array(AROUND_ALPHA) == "") || ($array(AROUND_BETA) == "") || ($array(AROUND_GAMMA) == "") || ($array(AROUND_EULER_RANGE) == "") } { WarningMessage "NOT SET: rotation function search (euler angles and range)" return 0 } } if { (([GetValue $arrayname MR_ROT_SEARCH] == "SEARCH_SIMPLE") && ( [GetValue $arrayname MR_MODE] == "ROT") && ( !($array(N_SIMPLE_SEARCH) == 0 && ($array(N_ENSEMBLE) == 0))) ) } { if { ($array(MR_ROT_SEARCH_ID) == "") } { WarningMessage "NOT SET: search ensemble" return 0 } if { ([lsearch -exact $array(ENSEMBLE_MENU_LIST) $array(MR_ROT_SEARCH_ID)] < 0) } { WarningMessage "The search ensemble is not in the defined list of ensembles" return 0 } } if { (([GetValue $arrayname MR_SEARCH] == "SEARCH_SIMPLE") && ( [GetValue $arrayname MR_MODE] == "AUTO") ) } { if { $array(N_SIMPLE_SEARCH) < 1 } { if { $array(N_ENSEMBLE) > 0 } { WarningMessage "NOT SET: search ensemble" return 0 } } } if { (([GetValue $arrayname MR_SEARCH] == "SEARCH_SIMPLE") && ( [GetValue $arrayname MR_MODE] == "AUTO") ) } { if { $array(N_SIMPLE_SEARCH) < 1 } { if { $array(N_ENSEMBLE) < 1 } { if { [GetValue $arrayname SET_SOL_FILE_NOTOB] == "" } { WarningMessage "NOT SET: ensembles and searches must be defined in SOL file" return 0 } } } } if { (([GetValue $arrayname MR_SEARCH] == "SEARCH_SIMPLE") && ( [GetValue $arrayname MR_MODE] == "AUTO") && ( !($array(N_SIMPLE_SEARCH) == 0 && ($array(N_ENSEMBLE) == 0))) ) } { for { set q 1 } { $q <= $array(N_SIMPLE_SEARCH) } { incr q } { if { ($array(MR_SIMPLE_ENSEMBLE_ID,$q) == "") } { WarningMessage "NOT SET: search ensemble" return 0 } if { ([lsearch -exact $array(ENSEMBLE_MENU_LIST) $array(MR_SIMPLE_ENSEMBLE_ID,$q)] < 0) } { WarningMessage "Search ensemble is not in the ensemble list" return 0 } } } if { (([GetValue $arrayname MR_SEARCH] == "SEARCH_OR") && ( [GetValue $arrayname MR_MODE] == "AUTO") ) } { if { $array(N_SEARCH) < 1 } { WarningMessage "NOT SET: search ensemble" return 0 } } if { (([GetValue $arrayname MR_SEARCH] == "SEARCH_OR") && ( [GetValue $arrayname MR_MODE] == "AUTO") ) } { for { set q 1 } { $q <= $array(N_SEARCH) } { incr q } { if { ($array(MR_FIRST_OR_ENSEMBLE_ID,$q) == "") } { WarningMessage "NOT SET: search ensemble" return 0 } if { ([lsearch -exact $array(ENSEMBLE_MENU_LIST) $array(MR_FIRST_OR_ENSEMBLE_ID,$q)] < 0) } { WarningMessage "Search ensemble is not in the ensemble list" return 0 } } } if { (([GetValue $arrayname MR_ROT_SEARCH] == "SEARCH_OR") && ( [GetValue $arrayname MR_MODE] == "ROT") ) } { for { set p 1 } { $p <= $array(N_ROT_SEARCH_EXTRA) } { incr p } { if { $array(MR_ROT_SEARCH_ID_EXTRA,$p) == "" } { WarningMessage "NOT SET: search ensemble" return 0 } if { ([lsearch -exact $array(ENSEMBLE_MENU_LIST) $array(MR_ROT_SEARCH_ID_EXTRA,$p)] < 0) } { WarningMessage "Search ensemble is not in the ensemble list" return 0 } } } if { (([GetValue $arrayname MR_SEARCH] == "SEARCH_OR") && ( [GetValue $arrayname MR_MODE] == "AUTO") ) } { for { set n 1 } { $n <= $array(N_SEARCH) } { incr n } { for { set p 1 } { $p <= $array(N_SEARCH_EXTRA,$n) } { incr p } { if { $array(MR_EXTRA_OR_ENSEMBLE_ID,[subst $n]_$p) == "" } { WarningMessage "NOT SET: search ensemble" return 0 } if { ([lsearch -exact $array(ENSEMBLE_MENU_LIST) $array(MR_EXTRA_OR_ENSEMBLE_ID,[subst $n]_$p)] < 0) } { WarningMessage "Search ensemble is not in the ensemble list" return 0 } } } } # Check for compulsory brute force translation function AROUND search parameters if { ([GetValue $arrayname MR_MODE] == "TRA") && ([GetValue $arrayname FTF_TARGET_OPTION] == "BRUTE") && ([GetValue $arrayname BTF_SEARCH_OPTION] == "AROUND") } { if { ($array(START_X) == "") || ($array(START_Y) == "") || ($array(START_Z) == "") || ($array(AROUND_COORD_RANGE) == "") } { WarningMessage "NOT SET: translation function search (coordinates and range)" return 0 } } # Check for compulsory brute force translation function REGION search parameters if { ([GetValue $arrayname MR_MODE] == "TRA") && ([GetValue $arrayname FTF_TARGET_OPTION] == "BRUTE") && ([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 "NOT SET: translation function search (coordinates and range)" return 0 } } # Check for compulsory brute force translation function LINE search parameters if { ([GetValue $arrayname MR_MODE] == "TRA") && ([GetValue $arrayname FTF_TARGET_OPTION] == "BRUTE") && ([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 "NOT SET: translation function search (coordinates and range)" return 0 } } if { ( [GetValue $arrayname MR_MODE] == "TRA" ) && \ ( $array(TRA_RLIST_FILE) == "" ) } { WarningMessage "NOT SET: translation function search (rlist file)" 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 MAP [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" } } } if { ([GetValue $arrayname SCATTERING] == "COMPONENT") } { for { set n 1 } { $n <= $array(N_COMPONENT) } { incr n } { if { $array(COMP_OPTION,$n) == "sequence file" } { append array(INPUT_FILES) " COMP_FILE,$n" } } } if { [GetValue $arrayname MR_MODE] == "TRA" } { append array(INPUT_FILES) " TRA_RLIST_FILE" } if { ([GetValue $arrayname MR_MODE] == "RNP") || ([GetValue $arrayname MR_MODE] == "PAK") } { append array(INPUT_FILES) " SET_SOL_FILE" } if { ([GetValue $arrayname MR_MODE] != "RNP") && ([GetValue $arrayname MR_MODE] != "PAK") && ([GetValue $arrayname SET_SOL_FILE_NOTOB] != "") } { append array(INPUT_FILES) " SET_SOL_FILE_NOTOB" } # 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(SPACGROUP_NUMBER) [GetSpaceGroupNumber $array(TEST_SPACEGROUP)] } else { set array(SPACGROUP_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_fractional { arrayname counter_component } { #------------------------------------------------------------------------ # The contents of the "Composition" folder, extending frame upvar #0 $arrayname array CreateLine line \ message "" \ label "Ensemble " \ widget COMP_ENSE_ID \ label " Fraction scattering " \ widget COMP_ENSE_FRAC -oblig } #------------------------------------------------------------------------ proc phaser_MR_component { 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 asu " \ 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 $counter_component in the asu" \ label "Number in asymmetric unit" \ widget ASYM -oblig \ toggle_display COMP_OPTION,$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 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 number of residues of protein/nucleic acid $counter_component" \ label "" \ widget COMP_OPTION -oblig \ widget COMP_NRES -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 NRES hide } #------------------------------------------------------------------------ proc phaser_MR_ensemble { arrayname counter_ensemble } { #------------------------------------------------------------------------ # Sets up the main ensembles definition folder, extending frame upvar #0 $arrayname array # Set a default name for ENSEMBLE_ID of ensemble1, ensemble2, ensemble3 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 $arrayname" \ -oblig \ message "Define the ensemble by PDB file(s) or MAP file" \ label "Define ensemble via" widget ENSEMBLE_OPTION \ toggle_display ENSEMBLE_OPTION,$counter_ensemble open MAP CreateLine line \ message "Enter unique identifier for ensemble #$counter_ensemble" \ label "Ensemble Name" widget ENSEMBLE_ID \ -command "update_phaser_MR_ensemble $arrayname" \ -oblig \ message "Define the ensemble by PDB file(s) or MAP file" \ label "Define ensemble via" widget ENSEMBLE_OPTION \ toggle_display ENSEMBLE_OPTION,$counter_ensemble open PDB \ widget TOG_HETATM label "Use HETATM atoms" OpenSubFrame frame -toggle_display ENSEMBLE_OPTION,$counter_ensemble open MAP 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_rot_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_ROT_SEARCH_ID_EXTRA } #------------------------------------------------------------------------ proc phaser_MR_simple_search { arrayname counter_simple_search } { #------------------------------------------------------------------------ # The auto search extending 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 search using " \ widget MR_SIMPLE_ENSEMBLE_ID \ message "The number of copies of the ensemble to look for" \ label " Number of copies to search for" \ widget MR_SIMPLE_ENSEMBLE_NUM } #------------------------------------------------------------------------ proc phaser_MR_or_search { arrayname counter_search } { #------------------------------------------------------------------------ # The auto search toggle frame code for adding extra search ensembles upvar #0 $arrayname array CreateLine line \ label "Perform search using " \ widget MR_FIRST_OR_ENSEMBLE_ID \ message "The number of copies of the ensemble to look for" \ label " Number of copies to search for" \ widget MR_FIRST_OR_ENSEMBLE_NUM CreateExtendingFrame N_SEARCH_EXTRA phaser_MR_or_search_extra \ "Add an alternative ensemble to use in the search" \ "Add alternative ensemble to test" \ [list MR_EXTRA_OR_ENSEMBLE_ID N_SEARCH_EXTRA] \ -counter $counter_search } #------------------------------------------------------------------------ proc phaser_MR_or_search_extra { arrayname counter_search_extra counter_search } { #------------------------------------------------------------------------ # The auto search extending frame code for adding extra ensembles to a search upvar #0 $arrayname array CreateLine line \ label " or ensemble" \ widget MR_EXTRA_OR_ENSEMBLE_ID } #------------------------------------------------------------------------ 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 #$counter_pdb" \ XYZIN DIR_XYZIN CreateLine line \ message "Specify RMS error in Angstrom, or \ via the sequence identity (percentage or a fraction)" \ label "Similarity of PDB #$counter_pdb to the target structure" \ widget RMS_OPTION widget RMS -oblig \ toggle_display RMS_OPTION,[subst $counter_ensemble]_$counter_pdb open [list "sequence identity" "rms difference" "low rms from id" "high rms from id"] hide CreateLine line \ message "Specify RMS error in Angstrom, or \ via the sequence identity (percentage or a fraction)" \ label "Similarity of PDB #$counter_pdb to the target structure" \ widget RMS_OPTION \ toggle_display RMS_OPTION,[subst $counter_ensemble]_$counter_pdb open [list "from pdb REMARK" ] hide # puts $array(RMS_OPTION,[subst $counter_ensemble]_$counter_pdb) # puts RMS_OPTION,[subst $counter_ensemble]_$counter_pdb } #------------------------------------------------------------------------ proc update_phaser_MR_ensemble { arrayname } { #------------------------------------------------------------------------ # This is called whenever the user clicks into the widget for an # ensemble name upvar #0 $arrayname array # It looks like an empty (redundant) procedure but is needed to ensure # that $array(N_ENSEMBLE) gets handed correctly to the menu procedure 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,$n)" } # Update ENSEMBLE_ID if an ensemble is deleted and its ENSEMBLE_ID # is still set to the default ensemble$counter_ensemble # (which will now be out by one (one too high)) # regexp as below on "ensemble1" produces j1_whole=ensemble1 # j2_root=ensemble # j3_num=1 if { $counter_ensemble > 0 } { for { set p 1 } { $p <= $array(N_ENSEMBLE) } { incr p } { if { [regexp "^(ensemble)(\[0-9\])$" $array(ENSEMBLE_ID,$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) "ensemble$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_tncs_use_and_valid {arrayname} { #------------------------------------------------------------------------ upvar #0 $arrayname array set array(TNCS_USE_AND_VALID) "1" if { [StringSame $array(MR_MODE) PAK] } { set array(TNCS_USE_AND_VALID) "0" } elseif { [StringSame $array(TNCS_USE) OFF] } { set array(TNCS_USE_AND_VALID) "0" } } #------------------------------------------------------------------------ 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_maca { arrayname counter_s } { #------------------------------------------------------------------------ global configure upvar #0 $arrayname array CreateLine line \ label " Anisotropic" \ widget MACA_ANIS \ label "Bins" \ widget MACA_BINS \ label "SolK" \ widget MACA_SOLK \ label "SolB" \ widget MACA_SOLB \ label "Number of Cycles" \ widget MACA_NCYC -width 5 } #------------------------------------------------------------------------ proc phaser_MR_macm { arrayname counter_s } { #------------------------------------------------------------------------ global configure upvar #0 $arrayname array CreateLine line \ label " Rotation" widget MACM_ROT \ label "Tranlation" widget MACM_TRA \ label "Bfactor" widget MACM_BFAC \ label "Vrms" widget MACM_VRMS \ label "EM cell" widget MACM_CELL \ label "Last" widget MACM_LAST \ label "NCYC" widget MACM_NCYC -width 5 } #------------------------------------------------------------------------ proc phaser_MR_task_window {arrayname} { #------------------------------------------------------------------------ upvar #0 $arrayname array global configure if { [CreateTaskWindow $arrayname \ "Maximum Likelihood Molecular Replacement"\ "Phaser" \ [ list "Define data" \ "Define ensembles (models)" \ "Define composition of the asymmetric unit" \ "Search parameters " \ "Additional Search parameters" \ "Expert parameters" \ "Output control" \ "Developer parameters" ] \ ] == 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 CreateLine line \ message "Number of processors (parallelization)" \ widget TOG_NJOBS -toggleon \ label "Number of processors "\ widget NJOBS \ label "(only relevant if phaser compiled with openmp option)" #=FILE=================================================================== # The "Define data" folder OpenFolder 1 MR_MODE 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 resolution_max RESOLUTION_AUTO_DMIN \ -setfileparam cell_1 CELL_1 \ -setfileparam cell_2 CELL_2 \ -setfileparam cell_3 CELL_3 \ -setfileparam cell_4 CELL_4 \ -setfileparam cell_5 CELL_5 \ -setfileparam cell_6 CELL_6 \ -setfileparam space_group_name FILE_SPACEGROUP \ -command "phaser_MR_set_test_space_group $arrayname" \ -command "phaser_MR_set_reso $arrayname" CreateLabinLine line \ "Select amplitude (F) and sigma (SIGF)" \ HKLIN_MAIN "F" F {NULL} \ -sigma "SIGF" SIGF {NULL} CreateLabinLine line \ "Select Phases and FOM for Phased Translation Function" \ HKLIN_MAIN "PHI" PHI [list PHIC PHIB PHWT PHI PHIDM] \ -dependent "FOM" FOM [list FOM FOMDM] \ -toggle_display FTF_TARGET_OPTION open [list PHASED] 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 \ label "; " \ widget TOG_SPACEGROUP -toggleon \ message "Run Phaser with a different space group" \ label "Run Phaser with space group" \ widget TEST_SPACEGROUP \ toggle_display MR_MODE open [list ROT RNP PAK] OpenSubFrame frame -toggle_display MR_MODE open [list AUTO TRA] CreateLine line \ message "Space group read from mtz file." \ label "Space group read from mtz file" \ varlabel FILE_SPACEGROUP \ label "; " \ message "Specify the space group(s) to run Phaser with" \ label "Run Phaser with" \ widget SPACEGROUP_OPTION CreateLine line \ widget TOG_SGAL_SORT -toggleon \ label "Test spacegroups in order of general occurrence in PDB" \ widget SGAL_SORT_ONOFF \ toggle_display SPACEGROUP_OPTION open [list SG_ALT SG_ALL] 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 ] CloseSubFrame CloseSubFrame # $line.l2 configure -width 7 -background $configure(COLOUR_BACKGROUND) #======================================================================== # The "Define ensembles" folder OpenFolder 2 open CreateToggleFrame N_ENSEMBLE phaser_MR_ensemble \ "Define another ensemble" \ "Ensemble #" \ "Add ensemble" \ [list ENSEMBLE_ID ENSEMBLE_OPTION HKLIN DIR_HKLIN ENSEMBLE_LABIN FC PHIC N_PDB ] \ -edit_proc edit_phaser_MR_ensemble \ -child phaser_MR_pdb #======================================================================== # The "Define composition of the asymmetric unit" folder OpenFolder 3 MR_MODE hide [list PAK ] open CreateLine line \ message "Total scattering of atoms in the asymmetric unit" \ label "Total scattering determined by "\ widget SCATTERING \ toggle_display SCATTERING hide SOLVENT CreateLine line \ message "Total scattering of atoms in the asymmetric unit" \ label "Total scattering determined by "\ widget SCATTERING \ widget SCATTERING_SOLVENT -oblig \ toggle_display SCATTERING open SOLVENT OpenSubFrame frame -toggle_display SCATTERING open COMPONENT hide CreateExtendingFrame N_COMPONENT phaser_MR_component \ "Define another protein or nucleic acid component" "Define another component" \ [list PROTDNA MW ASYM COMP_OPTION COMP_NRES COMP_FILE DIR_COMP_FILE ] CloseSubFrame OpenSubFrame frame -toggle_display SCATTERING open FRAC hide CreateExtendingFrame N_COMPONENT_FRAC phaser_MR_fractional \ "Define another protein or nucleic acid component" "Define another component" \ [list COMP_ENSE_ID COMP_ENSE_FRAC ] CloseSubFrame #======================================================================== # The "Search parameters" folder OpenFolder 4 open CreateLine line \ message "A SOL file is a Phaser search results file" \ label "Define known solutions from a SOL file" \ toggle_display MR_MODE open [list RNP PAK] hide CreateInputFileLine line \ "Define known solutions from a SOL file \ (Phaser search results file)" \ "SOL file" \ SET_SOL_FILE DIR_SET_SOL_FILE \ -toggle_display MR_MODE open [list RNP PAK] hide CreateLine line \ message "A .rlist file is a Phaser rotation search results file" \ label "Define orientations for translation search\ and any known solutions from a .rlist file" \ toggle_display MR_MODE open [list TRA ] hide CreateInputFileLine line \ "A .rlist file is a Phaser rotation search results file" \ ".rlist file" \ TRA_RLIST_FILE DIR_TRA_RLIST_FILE \ -toggle_display MR_MODE open [list TRA ] hide OpenSubFrame frame -toggle_display MR_MODE open [list ROT] hide # CreateLine line \ label "Allow search with alternative ensembles (models) for a single component of ASU" \ message "Set toggle on for OR search" \ widget MR_ROT_SEARCH CreateLine line \ message "Choose an ensemble to be used for the rotation search" \ label "Perform search using " \ widget MR_ROT_SEARCH_ID OpenSubFrame frame -toggle_display MR_ROT_SEARCH open SEARCH_OR hide CreateExtendingFrame N_ROT_SEARCH_EXTRA phaser_MR_rot_extra \ "Add an alternative ensemble to be searched for" \ "Add an alternative search ensemble" \ [list MR_ROT_SEARCH_ID_EXTRA] CloseSubFrame CloseSubFrame OpenSubFrame frame -toggle_display MR_MODE open AUTO hide # CreateLine line \ label "Allow search with alternative ensembles (models) for a single component of ASU" \ message "Set toggle on for OR search" \ widget MR_SEARCH OpenSubFrame frame -toggle_display MR_SEARCH open SEARCH_SIMPLE hide CreateExtendingFrame N_SIMPLE_SEARCH phaser_MR_simple_search \ "Add another ensemble to be searched for" \ "Add another search" \ [list MR_SIMPLE_ENSEMBLE_ID MR_SIMPLE_ENSEMBLE_NUM ] CloseSubFrame OpenSubFrame frame -toggle_display MR_SEARCH open SEARCH_OR hide CreateToggleFrame N_SEARCH phaser_MR_or_search \ "Perform another mr auto search" \ "Search #" \ "Add another search" \ [list MR_FIRST_OR_ENSEMBLE_ID MR_FIRST_OR_ENSEMBLE_NUM MR_EXTRA_OR_ENSEMBLE_ID N_SEARCH_EXTRA ] \ -child phaser_MR_or_search_extra CloseSubFrame CloseSubFrame #======================================================================== # The "Additional Search parameters" folder OpenFolder 5 closed CreateLine line \ label "No additional search parameters" -italic \ toggle_display MR_MODE open [list PAK RNP] hide CreateLine line \ label "Allow search with alternative ensembles (models) for a single component of ASU" \ message "Set toggle on for OR search" \ widget MR_SEARCH \ toggle_display MR_MODE open [list AUTO] hide CreateLine line \ label "Allow search with alternative ensembles (models) for a single component of ASU" \ message "Set toggle on for OR search" \ widget MR_ROT_SEARCH \ toggle_display MR_MODE open [list ROT] hide CreateLine line \ message "A SOL file is a Phaser search results file" \ label "Define any known solutions from a SOL file" \ toggle_display MR_MODE open [list AUTO ROT] hide CreateInputFileLine line \ "Define known solutions from a SOL file\ (Phaser search results file)" \ "SOL file" \ SET_SOL_FILE_NOTOB DIR_SET_SOL_FILE_NOTOB \ -notoblig \ -toggle_display MR_MODE open [list AUTO ROT] hide OpenSubFrame frame -toggle_display MR_MODE open [list AUTO ROT] hide CreateLine line \ message "TARGET: select the rotation target function to be used" \ widget TOG_FRF_TARGET -toggleon \ label "Rotation target function" \ widget FRF_TARGET_OPTION OpenSubFrame frame -toggle_display FRF_TARGET_OPTION open BRUTE hide CreateLine line \ message "Select to perform a full or restricted search" \ label "Search" \ widget BRF_SEARCH_OPTION \ message "Restrict the search to region around this set of Euler angles" \ label "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 "Range" \ widget AROUND_EULER_RANGE -oblig \ toggle_display BRF_SEARCH_OPTION open AROUND CreateLine line \ message "Select to perform a full or restricted search" \ label "Search" \ widget BRF_SEARCH_OPTION \ toggle_display BRF_SEARCH_OPTION open FULL CloseSubFrame CloseSubFrame OpenSubFrame frame -toggle_display MR_MODE open [list TRA AUTO] hide CreateLine line \ message "TARGET: select the translation target function to be used" \ widget TOG_FTF_TARGET -toggleon \ label "Translation target function" \ widget FTF_TARGET_OPTION OpenSubFrame frame -toggle_display FTF_TARGET_OPTION open BRUTE 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 \ label "translation search" CreateLine line \ message "Select the coordinate system" \ label "Search point/line/volume defined in" widget COORD_SYS label "coordinates" \ toggle_display BTF_SEARCH_OPTION hide FULL CreateLine line \ label "Search around point" \ label "X" widget START_X -oblig \ label "Y" widget START_Y -oblig \ label "Z" widget START_Z -oblig \ message "Range around point to search" \ label "with search range" widget AROUND_COORD_RANGE -oblig \ label "Angstroms" \ toggle_display BTF_SEARCH_OPTION open AROUND CreateLine line \ label "Search box top corner" \ label "X" widget START_X -oblig -width 6 \ label "Y" widget START_Y -oblig -width 6 \ label "Z" widget START_Z -oblig -width 6 \ label "bottom corner" \ label "X" widget END_X -oblig -width 6 \ label "Y" widget END_Y -oblig -width 6 \ label "Z" widget END_Z -oblig -width 6 \ toggle_display BTF_SEARCH_OPTION open [list REGION ] hide CreateLine line \ label "Search along line start" \ label "X" widget START_X -oblig \ label "Y" widget START_Y -oblig \ label "Z" widget START_Z -oblig \ label "end" \ label "X" widget END_X -oblig \ label "Y" widget END_Y -oblig \ label "Z" widget END_Z -oblig \ toggle_display BTF_SEARCH_OPTION open [list LINE] hide CloseSubFrame CloseSubFrame #======================================================================== # The "Expert parameters" folder OpenFolder 6 closed CreateLine line \ label "Warning: allow phaser to optimize the resolution" -italic \ toggle_display MR_MODE hide [list PAK] 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 [list PAK] CreateLine line \ message "Default is to take all data in mtz file" \ widget TOG_RESOLUTION_AUTO -toggleon \ label "High resolution for final refinement" \ message "Enter dmin, in Angstroms" \ widget RESOLUTION_AUTO_DMIN \ label "A" \ toggle_display MR_MODE open [list AUTO] hide OpenSubFrame frame -toggle_display SEARCH_METHOD open FAST hide CreateLine line \ message "Search to high resolution if high TFZ not found with default resolution" \ widget TOG_SEARCH_HIRES -toggleon \ label "Search high resolution if low TFZ " widget SEARCH_HIRES \ toggle_display MR_MODE open [list AUTO] hide CloseSubFrame CreateLine line \ label "Warning: Do not toggle checkboxes unless changing parameter from default" -italic OpenSubFrame frame -toggle_display MR_MODE open [list AUTO PAK] hide CreateLine line \ message "Solutions with the lowest number of clashes will be saved \ if less than the max allowed (default 10)" \ widget TOG_PACK -toggleon \ label "Packing criterion " \ widget PACK_OPTION \ label "Allow " \ widget PACK_ALLOWED_CLASHES \ toggle_display PACK_OPTION open BEST CreateLine line \ message "All solutions will be saved no matter how many clashes" \ widget TOG_PACK -toggleon \ label "Packing criterion " \ widget PACK_OPTION \ toggle_display PACK_OPTION open ALL CreateLine line \ message "Default for allowed C-alpha clashes is 10;\ increase for low-homology models" \ widget TOG_PACK -toggleon \ label "Packing criterion " \ widget PACK_OPTION \ label "Allow " \ widget PACK_ALLOWED_CLASHES \ toggle_display PACK_OPTION open ALLOWED CreateLine line \ message "Default for allowed C-alpha clashes is 10;\ increase for low-homology models" \ widget TOG_PACK -toggleon \ label "Packing criterion " \ widget PACK_OPTION \ label "Allow " \ widget PACK_ALLOWED_CLASHES \ toggle_display PACK_OPTION open PERCENT CreateLine line \ widget TOG_PACK_QUICK -toggleon \ label "Quick Packing " \ widget PACK_QUICK_ONOFF \ toggle_display PACK_OPTION hide ALL CloseSubFrame OpenSubFrame frame -toggle_display MR_MODE open [list AUTO ROT] hide CreateLine line \ message "Final selection criterion for peaks from rotation searches" \ widget TOG_FINAL_ROT -toggleon \ label "Rotation search peak selection" \ message "Default 75 percent" \ widget FINAL_OPTION_ROT \ message "Enter the cutoff" \ widget FINAL_SIGMA_ROT \ toggle_display FINAL_OPTION_ROT hide [list ALL] open CreateLine line \ message "Final selection criterion for peaks from rotation searches" \ widget TOG_FINAL_ROT -toggleon \ label "Rotation search peak selection" \ message "Default 75 percent" \ widget FINAL_OPTION_ROT \ toggle_display FINAL_OPTION_ROT open [list ALL] hide CloseSubFrame OpenSubFrame frame -toggle_display MR_MODE open [list AUTO TRA] hide CreateLine line \ message "Final selection criterion for peaks from translation searches" \ widget TOG_FINAL_TRA -toggleon \ label "Translation search peak selection" \ message "Default 75 percent" \ widget FINAL_OPTION_TRA \ message "Enter the cutoff" \ widget FINAL_SIGMA_TRA \ toggle_display FINAL_OPTION_TRA hide [list ALL] open CreateLine line \ message "Final selection criterion for peaks from translation searches" \ widget TOG_FINAL_TRA -toggleon \ label "Translation search peak selection" \ message "Default 75 percent" \ widget FINAL_OPTION_TRA \ toggle_display FINAL_OPTION_TRA open [list ALL] hide CloseSubFrame CreateLine line \ message "Select whether clustered or raw peaks are saved" \ widget TOG_PEAKS_ROT_CLUSTER -toggleon \ label "Rotation clustering" \ widget PEAKS_ROT_CLUSTER \ toggle_display MR_MODE open [list AUTO ROT] CreateLine line \ message "Select whether clustered or raw peaks are saved" \ widget TOG_PEAKS_TRA_CLUSTER -toggleon \ label "Translation clustering" \ widget PEAKS_TRA_CLUSTER \ toggle_display MR_MODE open [list AUTO TRA] OpenSubFrame frame -toggle_display MR_MODE open [list AUTO] hide CreateLine line \ message "Choose whether to purge the solutions from RNP" \ widget TOG_PURGE_RNP -toggleon \ label "Purge refinement peaks" \ widget PURGE_RNP_ONOFF \ label " percent cutoff" \ widget PURGE_RNP_PERCENT \ label "but with maximum number " \ widget PURGE_RNP_NUMBER -width 5 \ toggle_display PURGE_RNP_ONOFF open ON CreateLine line \ message "Choose whether to purge the solutions from RNP" \ widget TOG_PURGE_RNP -toggleon \ label "Purge refinement peaks" \ widget PURGE_RNP_ONOFF \ toggle_display PURGE_RNP_ONOFF open OFF CreateLine line \ message "Target for expected LLG given model completeness and RMS" \ widget TOG_USE_ELLG -toggleon \ label "Use \"expected LLG\" criteria in decision making" widget USE_ELLG label " Target LLG " widget ELLG_TARGET \ toggle_display USE_ELLG open ON hide CreateLine line \ message "Target for expected LLG given model completeness and RMS" \ widget TOG_USE_ELLG -toggleon \ label "Use \"expected LLG\" criteria in decision making" widget USE_ELLG \ toggle_display USE_ELLG open OFF hide CloseSubFrame OpenSubFrame frame -toggle_display MR_MODE hide [list PAK] open CreateLine line \ message "TNCS: use or ignore translational NCS if present" \ widget TOG_TNCS_USE -toggleon \ label "Use translational NCS if present " \ widget TNCS_USE -command "phaser_MR_tncs_use_and_valid $arrayname" \ toggle_display TNCS_USE open ON CreateLine line \ label "TNCS: " \ widget TOG_TNCS_NMOL -toggleon \ label "Number of assemblies related by TNCS " \ widget TNCS_NMOL \ toggle_display TNCS_USE open ON CreateLine line \ message "TNCS: Parameters for identifying TNCS from Patterson" \ label "TNCS: " \ widget TOG_TNCS_PATT_PERCENT -toggleon \ label "Minimum percent of Patterson origin peak " \ widget TNCS_PATT_PERCENT \ toggle_display TNCS_USE open ON CreateLine line \ message "TNCS: translation vector in fractional coordinates" \ label "TNCS: " \ widget TOG_TNCS_TRA_VECTOR -toggleon \ label "Fix vector " \ widget TNCS_TRA_VECTOR_X \ widget TNCS_TRA_VECTOR_Y \ widget TNCS_TRA_VECTOR_Z label "(fractional coordinates)" \ toggle_display TNCS_USE open ON CreateLine line \ message "TNCS: use or ignore translational NCS if present" \ widget TOG_TNCS_USE -toggleon \ label "Use translational NCS if present " \ widget TNCS_USE -command "phaser_MR_tncs_use_and_valid $arrayname" \ toggle_display TNCS_USE open OFF CloseSubFrame OpenSubFrame frame -toggle_display MR_MODE open [list AUTO ] CreateLine line \ message "Use FAST if you expect the TFZ to be high for each copy" \ widget TOG_SEARCH_METHOD -toggleon \ label "Search method for many copies in ASU" \ widget SEARCH_METHOD \ label "Deep rotation search" widget SEARCH_DEEP \ -command "update_phaser_MR_search $arrayname" \ message "Percentage to Reduce RF peak cutoff on 2nd pass" \ label "Down" widget SEARCH_DOWN_PERC -width 5 \ -command "update_phaser_MR_search $arrayname" \ label "%" \ message "Value for reducing cutoff" \ toggle_display SEARCH_METHOD open FAST hide CreateLine line \ message "Use FAST if you expect the TFZ to be high for each copy" \ widget TOG_SEARCH_METHOD -toggleon \ label "Search method for many copies in ASU" \ widget SEARCH_METHOD \ label "Permute search order" widget PERMUTATIONS_ONOFF \ -command "update_phaser_MR_search $arrayname" \ toggle_display SEARCH_METHOD open FULL hide CreateLine line \ message "Refine rotation angles" \ widget TOG_ROTREF -toggleon \ label "Refine rotations prior to translation function" \ widget ROTREF CloseSubFrame OpenSubFrame frame -toggle_display MR_MODE open [list AUTO PAK TRA] CreateLine line \ message "Controls how TFZ is used in decision making" \ widget TOG_ZSCORE -toggleon \ label "Use Z-score (TFZ)" widget ZSCORE_USE \ label "TFZ solved " widget ZSCORE_SOLVED \ label "and also half highest" widget ZSCORE_HALF \ toggle_display ZSCORE_USE open ON hide CreateLine line \ message "Controls how TFZ is used in decision making" \ widget TOG_ZSCORE -toggleon \ label "Use Z-score (TFZ)" widget ZSCORE_USE \ toggle_display ZSCORE_USE open OFF hide CloseSubFrame #======================================================================== # The "Output control" folder OpenFolder 7 MR_MODE closed CreateLine line \ message "VERBOSE: more information included in log file than by default" \ widget TOG_VERBOSE \ label "Verbose output to log file" \ CreateLine line \ message "DEBUG: debugging information included in log file than by default" \ widget TOG_VERBOSE_EXTRA \ label "Debug output to log file" CreateLine line \ message "Default number of top pdbfiles and mtzfiles is 1" \ widget TOG_TOPF -toggleon \ label "Number of top solutions to output as PDB and MTZ files"\ widget XYZOUT_NPDB CreateLine line \ message "Output the results in a .sol file" \ widget TOG_KEYWDS -toggleon \ label "SOL file output" \ widget KEYWDS_ONOFF \ toggle_display MR_MODE hide [list ROT] CreateLine line \ message "Output the results in a .rlist file" \ widget TOG_KEYWDS -toggleon \ label "RLIST file output" \ widget KEYWDS_ONOFF \ toggle_display MR_MODE open [list ROT] hide CreateLine line \ message "Controls output of PDB files containing potential solutions." \ widget TOG_XYZOUT -toggleon \ label "PDB file output" \ widget XYZOUT_ONOFF CreateLine line \ message "Controls output of MTZ files with phase information from solutions." \ widget TOG_HKLOUT -toggleon \ label "MTZ file output" \ widget HKLOUT_ONOFF \ toggle_display MR_MODE hide [list PAK ] #======================================================================== # The "Developer parameters" folder # OpenFolder 8 closed CreateLine line \ label "Do not alter these parameters" -italic OpenSubFrame frame -toggle_display MR_MODE open [list AUTO ROT] hide CreateLine line \ message "Choose whether to purge the solutions from RF " \ widget TOG_PURGE_ROT -toggleon \ label "Purge rotation peaks" \ widget PURGE_ROT_ONOFF \ label " percent cutoff" \ widget PURGE_ROT_PERCENT \ label "but with maximum number " \ widget PURGE_ROT_NUMBER -width 5\ toggle_display PURGE_ROT_ONOFF open ON CreateLine line \ message "Choose whether to purge the solutions from RF" \ widget TOG_PURGE_ROT -toggleon \ label "Purge rotation peaks" \ widget PURGE_ROT_ONOFF \ toggle_display PURGE_ROT_ONOFF open OFF CloseSubFrame OpenSubFrame frame -toggle_display MR_MODE open [list AUTO TRA] hide CreateLine line \ message "Choose whether to purge the solutions from TF" \ widget TOG_PURGE_TRA -toggleon \ label "Purge translation peaks" \ widget PURGE_TRA_ONOFF \ label " percent cutoff" \ widget PURGE_TRA_PERCENT \ label "but with maximum number " \ widget PURGE_TRA_NUMBER -width 5 \ toggle_display PURGE_TRA_ONOFF open ON CreateLine line \ message "Choose whether to purge the solutions from TF" \ widget TOG_PURGE_TRA -toggleon \ label "Purge translation peaks" \ widget PURGE_TRA_ONOFF \ toggle_display PURGE_TRA_ONOFF open OFF CloseSubFrame CreateLine line \ message "Select whether or not to rescore fast search solutions" \ widget TOG_RESCORE_ROT -toggleon \ label "Rescoring rotation" \ widget RESCORE_ONOFF_ROT \ toggle_display MR_MODE open [list AUTO ROT] hide CreateLine line \ message "Select whether or not to rescore fast search solutions" \ widget TOG_RESCORE_TRA -toggleon \ label "Rescoring translation" \ widget RESCORE_ONOFF_TRA \ toggle_display MR_MODE open [list AUTO TRA] hide CreateLine line \ message "BINS: specify the binning for the data reflections"\ widget TOG_BINS -toggleon \ label "Bins for Data: Min" widget BINS_L label "Max" widget BINS_H label "Width" widget BINS_W \ toggle_display MR_MODE hide [list PAK ] CreateLine line \ message "BINS: specify the binning for the calculated ensemble reflections"\ widget TOG_BINS_ENSE -toggleon \ label "Bins for Ensemble: Min" widget BINS_ENSE_L label "Max" widget BINS_ENSE_H label "Width" widget BINS_ENSE_W \ toggle_display MR_MODE hide [list PAK ] 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)" \ widget BOXSCALE \ toggle_display MR_MODE hide [list PAK] 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_SPHERE \ label "LMIN " \ widget CLMN_INNER \ label "LMAX " \ widget CLMN_OUTER \ toggle_display MR_MODE open [list AUTO ROT ] hide OpenSubFrame frame -toggle_display MR_MODE hide [list PAK] open CreateLine line \ message "Refinement macrocyles" \ widget TOG_ANISO -toggleon \ label "Anisotropic refinement protocol" \ widget MACA_PROTOCOL OpenSubFrame frame \ -toggle_display MACA_PROTOCOL open CUSTOM hide CreateExtendingFrame N_MACA phaser_MR_maca \ "Customize the anisotropic refinement" \ "Add another anisotropic macrocycle" \ [list MACA_ANIS MACA_BINS MACA_SOLK MACA_SOLB MACA_NCYC ] CloseSubFrame CloseSubFrame OpenSubFrame frame -toggle_display MR_MODE open [list AUTO RNP] hide CreateLine line \ message "Refinement macrocyles" \ widget TOG_MACM -toggleon \ label "Molecular replacement refinement protocol" \ widget MACM_PROTOCOL OpenSubFrame frame \ -toggle_display MACM_PROTOCOL open CUSTOM hide CreateExtendingFrame N_MACM phaser_MR_macm \ "Customize the MR refinement" \ "Add another MR macrocycle" \ [list MACM_ROT MACM_TRA MACM_BFAC MACM_VRMS MACM_CELL MACM_LAST MACM_NCYC ] CloseSubFrame CloseSubFrame OpenSubFrame frame -toggle_display MR_MODE hide [list PAK] open 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 "Outliers with a probability \ less than the cutoff are rejected" \ widget OUTLIER_PROB -width 10 \ 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 "PACKING: sampling of search space" \ widget TOG_PACK_DISTANCE -toggleon \ label "Distance for the packing test" \ message "Distance between marker atoms for the clash test " \ widget PACK_DISTANCE \ toggle_display MR_MODE open [list AUTO PAK] CreateLine line \ message "PACKING: sampling of search space" \ widget TOG_PACK_TRACE -toggleon \ label "Use Trace atom for packing analysis " \ message "Use C-alphas in proteins, P for RNA/DNA for clash test" \ widget PACK_TRACE \ label "Trace maximum " \ widget PACK_TRACE_MAX \ toggle_display MR_MODE open [list AUTO PAK] CreateLine line \ widget TOG_PACK_COMPACT -toggleon \ label "Pack molecules into compact group " \ widget PACK_COMPACT_ONOFF \ toggle_display MR_MODE open [list AUTO PAK] CreateLine line \ message "PTGROUP: tolerances for detection of model symmetry" \ widget TOG_PTGR_SEQ -toggleon \ label "Point Group Minimum Sequence Tolerances: Coverage" \ widget PTGR_COVERAGE \ label "Identity" \ widget PTGR_IDENTITY \ toggle_display MR_MODE open [list AUTO RNP PAK] CreateLine line \ message "PTGROUP: tolerances for detection of model symmetry" \ widget TOG_PTGR_XYZ -toggleon \ label "Point Group Maximum Coordinate Tolerances: RMS" \ widget PTGR_RMSD -width 6 \ label "Angular" \ widget PTGR_TOL_ANG -width 6 \ label "Spatial" \ widget PTGR_TOL_SPC -width 6 \ toggle_display MR_MODE open [list AUTO RNP] CreateLine line \ widget TOG_SEARCH_ORDER_AUTO -toggleon \ label "Determine ensemble search order automatically" \ widget SEARCH_ORDER_AUTO_ONOFF \ toggle_display MR_MODE open [list AUTO ] CreateLine line \ message "SAMPLING: sampling of search space" \ widget TOG_SAMP_ROT -toggleon \ label "Sampling for rotation search" \ message "Sampling for rotation search given in degrees" \ widget SAMPLING_ROT \ toggle_display MR_MODE open [list AUTO ROT] CreateLine line \ message "TARGET: select the fast rotation function type to be used" \ widget TOG_FRF_TARGET_TYPE -toggleon \ label "Fast rotation function type" \ widget FRF_TARGET_TYPE_OPTION \ toggle_display MR_MODE open [list AUTO ROT] CreateLine line \ message "SAMPLING: sampling of search space" \ widget TOG_SAMP_TRA -toggleon \ label "Sampling for translation search" \ message "Sampling for translation search given in Angstroms" \ widget SAMPLING_TRA \ toggle_display MR_MODE open [list AUTO TRA] CreateLine line \ message "TARGET: select the fast translation function type to be used" \ widget TOG_FTF_TARGET_TYPE -toggleon \ label "Fast translation function type" \ widget FTF_TARGET_TYPE_OPTION \ toggle_display MR_MODE open [list AUTO TRA] CreateLine line \ message "RESHARPEN: B-factor added back to map coefficients" \ widget TOG_RESHARPEN -toggleon \ label "Resharpening percentage " \ message "Resharpening percentage " \ widget RESHARPEN_PERC \ toggle_display MR_MODE hide [list PAK] CreateLine line \ message "SOLPARAMETERS: set the solvent parameters for the ensembling" \ widget TOG_SOLP -toggleon \ label "Solvent parameters for SigmaA: Ksol " widget SOLP_FSOL \ label " Bsol " widget SOLP_BSOL \ label " Minimum " widget SOLP_SIGA_MIN \ toggle_display MR_MODE hide [list PAK] CreateLine line \ message "SOLPARAMETERS: set the solvent parameters for the ensembling" \ widget TOG_BULK_SOLP -toggleon \ label "Solvent parameters for Bulk Mask: Use " widget SOLP_BULK_USE \ label " Ksol " widget SOLP_BULK_FSOL \ label " Bsol " widget SOLP_BULK_BSOL \ toggle_display MR_MODE hide [list PAK] CreateLine line \ message "Controls how TFZ is used in decision making" \ widget TOG_ZSCORE_HIGH -toggleon \ label "High TFZ minimum for terminating deep search of RF peaks" widget ZSCORE_HIGH \ toggle_display ZSCORE_USE open ON hide OpenSubFrame frame -toggle_display TNCS_USE_AND_VALID open 1 CreateLine line \ message "TNCS: refine TNCS rotation angles starting from sampling grid" \ label "TNCS: " \ widget TOG_TNCS_ROT_GRID -toggleon \ label "Refine TNCS rotation starting from angles on a grid " \ widget TNCS_ROT_GRID CreateLine line \ message "TNCS: rotation angle in degrees, perturbations around X Y and Z" \ label "TNCS: " \ widget TOG_TNCS_ROT_ANGLE -toggleon \ label "Initial TNCS rotation " \ widget TNCS_ROT_ANGLE_X \ widget TNCS_ROT_ANGLE_Y \ widget TNCS_ROT_ANGLE_Z label "Degrees (XYZ perturbations)" \ toggle_display TNCS_ROT_GRID open ON CreateLine line \ message "TNCS: rotation range" \ label "TNCS: " \ widget TOG_TNCS_ROT_RANGE -toggleon \ label "Range of angles to sample to find initial TNCS rotation " \ widget TNCS_ROT_RANGE \ label "Degrees" \ toggle_display TNCS_ROT_GRID open ON CreateLine line \ message "TNCS: rotation range" \ label "TNCS: " \ widget TOG_TNCS_ROT_SAMPLING -toggleon \ label "Sampling of angles to find initial TNCS rotation " \ widget TNCS_ROT_SAMPLING \ label "Degrees" \ toggle_display TNCS_ROT_GRID open ON CreateLine line \ message "TNCS: rotation angle in degrees, perturbations around X Y and Z" \ label "TNCS: " \ widget TOG_TNCS_ROT_ANGLE -toggleon \ label "Fixed rotation between TNCS related molecules " \ widget TNCS_ROT_ANGLE_X \ widget TNCS_ROT_ANGLE_Y \ widget TNCS_ROT_ANGLE_Z label "Degrees" \ toggle_display TNCS_ROT_GRID open OFF CreateLine line \ message "TNCS: RMSD between TNCS related molecules" \ label "TNCS: " \ widget TOG_TNCS_VAR_RMSD -toggleon \ label "RMSD between TNCS related molecules " \ widget TNCS_VAR_RMSD \ label "Angstroms" CreateLine line \ message "TNCS: Fraction of asymmetric unit obeying TNCS" \ label "TNCS: " \ widget TOG_TNCS_VAR_FRAC -toggleon \ label "Fraction of asymmetric unit obeying TNCS " \ widget TNCS_VAR_FRAC CreateLine line \ message "TNCS: Parameters for identifying TNCS from Patterson" \ label "TNCS: " \ widget TOG_TNCS_PATT_RESO -toggleon \ label "Patterson high resolution " \ widget TNCS_PATT_HIRES \ label "low resolution " \ widget TNCS_PATT_LORES CreateLine line \ message "TNCS: Parameters for identifying TNCS from Patterson" \ label "TNCS: " \ widget TOG_TNCS_PATT_DISTANCE -toggleon \ label "Minimum length of TNCS vector " \ widget TNCS_PATT_DISTANCE CloseSubFrame } #use puts to output debugging info to screen