# ======================================================================= # phaser_EP.tcl -- # # Phaser SAD pipeline # # CCP4Interface # # ======================================================================= #------------------------------------------------------------------------------ proc phaser_EP_prereq { } { #------------------------------------------------------------------------------ if { ![file exists [FindExecutable phaser]] } { return 0 } return 1 } #------------------------------------------------------------------------ proc phaser_EP_setup { typedefVar arrayname } { #------------------------------------------------------------------------ upvar #0 $typedefVar typedef upvar #0 $arrayname array DefineMenu _mode_ep [list "Single-wavelength anomalous dispersion (SAD)" \ "SAD with molecular replacement partial structure"] \ [list "SAD" "MRSAD"] DefineMenu _composition_option \ [ list "average solvent content for protein crystal" "solvent content of protein crystal" "components in asymmetric unit" ] \ [ list "AVERAGE" "SOLVENT" "COMPONENT" ] DefineMenu _protnucleic \ [list "protein" "nucleic acid" ] [list "PROTEIN" "NUCLEIC" ] DefineMenu _rmsid_option \ [list "rms difference" "sequence identity" ] [list "RMS" "IDENT" ] DefineMenu _clash_option \ [list "by optical resolution" "by fixed distance" ] [list "DEFAULT" "DISTANCE" ] DefineMenu _coord_frac \ [list "fractional" "orthogonal" ] [list "FRAC" "ORTH" ] DefineMenu _llgc_complete \ [list "on: all atom types" "off" "on: select atom types" ] [list "DEFAULT" "OFF" "ON" ] DefineMenu _scat_edge\ [list "only if near edge" "off" "on" ] [list "EDGE" "OFF" "ON" ] DefineMenu _llgc_method \ [list "all atomtype LLG-maps" "imaginary LLG-map only"] [list "ATOMTYPE" "IMAGINARY" ] DefineMenu _pdb_mtz_option \ [list "pdb" "mtz"] [list "PDB" "MTZ" ] DefineMenu _atom_search_option \ [list "SHELXD" "HYSS"] [list "SHELXD" "HYSS" ] DefineMenu _scat_option \ [list "at CuK-alpha wavelength" "at other wavelength" "by fluorescence scan" "explicitly by atomtype"] [list "CUKA" "LAMBDA" "MEASURED" "ATOMTYPE"] DefineMenu _atom_option \ [list "run phenix.hyss" "run ShelxC/D" "in PDB file" "in HA file" "in SOL file" "entered below"] \ [list "HYSS" "SHELXD" "PDB" "HA" "SOL" "MANUAL" ] DefineMenu _atom_option_short \ [list "in PDB file" "in HA file" "in SOL file" "entered below"] \ [list "PDB" "HA" "SOL" "MANUAL" ] DefineMenu _bfactor_option \ [list "Wilson B" "Entered" ] \ [list "WILSON" "VALUE" ] DefineMenu _rms_option \ [list "rms difference" "sequence identity" ] [list "RMS" "IDENT" ] DefineMenu _hand_option \ [list "Original" "Change" "Both"] [list "OFF" "ON" "BOTH" ] set typedef(_onoff) \ { menu { "on" "off" } { ON OFF } } set typedef(_mwseqnres_option) \ { menu { "molecular weight" "sequence file" "number of residues" } { "MW" "FASTA" "NRES"} } set typedef(_protocol) \ { menu { "default" "none (fix)" "custom" "all (ref)"} { "DEFAULT" "OFF" "CUSTOM" "ALL"} } set typedef(_hyss_search) \ { menu { "fast" "full"} { "FAST" "FULL"} } set typedef(_mtz_label_fo) { mtz_label {F} Unassigned H } return 1 } #------------------------------------------------------------------------ proc phaser_EP_run { arrayname } { #------------------------------------------------------------------------ upvar #0 $arrayname array set array(RUNHYSS) 0 set array(RUNSHELXD) 0 if { ([GetValue $arrayname RUNBUCCANEER] == "1") || [GetValue $arrayname EP_SAMR] == "1"} { if { ($array(FPwrk) == "Unassigned")} { WarningMessage "F mtz column is Unassigned" return 0 } if { ($array(SIGFPwrk) == "Unassigned")} { WarningMessage "SIGF mtz column is Unassigned" return 0 } if { ($array(FREER) == "Unassigned")} { WarningMessage "Free R flag mtz column is Unassigned" return 0 } } if { [GetValue $arrayname EP_SAMR] == "0"} { if { ($array(Fp_SAD) == "Unassigned") || ($array(Fn_SAD) == "Unassigned") } { WarningMessage "F mtz column is Unassigned" return 0 } if { ($array(SIGFp_SAD) == "Unassigned") || ($array(SIGFn_SAD) == "Unassigned") } { WarningMessage "SIGF mtz column is Unassigned" return 0 } } if { [GetValue $arrayname EP_MODE] == "SAD" && [GetValue $arrayname HA_SITES_OPTION_SAD] == "HYSS" } { set array(RUNHYSS) 1 if { ![file exists [FindExecutable phenix.hyss]] } { WarningMessage "phenix.hyss not installed" return 0 } } #puts "$array(RUNHYSS)" if { [GetValue $arrayname EP_MODE] == "SAD" && [GetValue $arrayname HA_SITES_OPTION_SAD] == "SHELXD" } { set array(RUNSHELXD) 1 if { ![file exists [FindExecutable shelxd]] } { WarningMessage "shelxd not installed" return 0 } if { ![file exists [FindExecutable shelxc]] } { WarningMessage "shelxc not installed" return 0 } } #Define data if { $array(HKLIN) == "" } { WarningMessage "NOT SET: mtz reflection data file" return 0 } if { ($array(WAVELENGTH) == 0) } { WarningMessage "NOT SET: Wavelength must be greater than zero" return 0 } if { ([GetValue $arrayname TOG_SCAT_MEASURED] == "1") } { if { ([GetValue $arrayname SCAT_TYPE] == "")} { WarningMessage "NOT SET: scattering type for fluorescence scan" return 0 } if { ([GetValue $arrayname SCAT_FP] == "")} { WarningMessage "NOT SET: f\' value for fluorescence scan" return 0 } if { ([GetValue $arrayname SCAT_FDP] == "")} { WarningMessage "NOT SET: f\" value for fluorescence scan" return 0 } } #Define Atoms if { ([GetValue $arrayname EP_MODE] == "SAD") } { if { ([GetValue $arrayname HA_SITES_OPTION_SAD] == "MANUAL") } { for { set n 1 } { $n <= $array(N_HA_SAD) } { incr n } { if { $array(HA_ATOM_TYPE_SAD,$n) == "" } { WarningMessage "NOT SET: atom type or cluster name for site # $n" return 0 } if { ($array(HA_ATOM_X_SAD,$n) == "") || ($array(HA_ATOM_Y_SAD,$n) == "") || ($array(HA_ATOM_Z_SAD,$n) == "") } { WarningMessage "NOT SET: coordinates for site # $n" return 0 } if { $array(HA_ATOM_O_SAD,$n) == "" } { WarningMessage "NOT SET: occupancy for site # $n" return 0 } } } } if { ([GetValue $arrayname EP_MODE] == "MRSAD") } { if { ([GetValue $arrayname HA_SITES_OPTION_MRSAD] == "MANUAL") } { for { set n 1 } { $n <= $array(N_HA_MRSAD) } { incr n } { if { $array(HA_ATOM_TYPE_MRSAD,$n) == "" } { WarningMessage "NOT SET: atom type or cluster name for site # $n" return 0 } if { ($array(HA_ATOM_X_MRSAD,$n) == "") || ($array(HA_ATOM_Y_MRSAD,$n) == "") || ($array(HA_ATOM_Z_MRSAD,$n) == "") } { WarningMessage "NOT SET: coordinates for site # $n" return 0 } if { $array(HA_ATOM_O_MRSAD,$n) == "" } { WarningMessage "NOT SET: occupancy for site # $n" return 0 } } } } if { ([GetValue $arrayname EP_MODE] == "SAD") } { if { ([GetValue $arrayname HA_SITES_OPTION_SAD] == "HA") } { if { $array(HA_FILE_HA_SAD) == "" } { WarningMessage "NOT SET: HA file for sites" return 0 } } if { ([GetValue $arrayname HA_SITES_OPTION_SAD] == "PDB") } { if { $array(HA_FILE_PDB_SAD) == "" } { WarningMessage "NOT SET: PDB file for sites" return 0 } } if { ([GetValue $arrayname HA_SITES_OPTION_SAD] == "SOL") } { if { $array(HA_FILE_SOL_SAD) == "" } { WarningMessage "NOT SET: SOL file for sites" return 0 } } } if { ([GetValue $arrayname EP_MODE] == "MRSAD") } { if { ([GetValue $arrayname TOG_ADDITIONAL_ATOMS] == "1") } { if { ([GetValue $arrayname HA_SITES_OPTION_MRSAD] == "HA") } { if { $array(HA_FILE_HA_SAD) == "" } { WarningMessage "NOT SET: HA file for sites" return 0 } } if { ([GetValue $arrayname HA_SITES_OPTION_MRSAD] == "PDB") } { if { $array(HA_FILE_PDB_SAD) == "" } { WarningMessage "NOT SET: PDB file for sites" return 0 } } if { ([GetValue $arrayname HA_SITES_OPTION_MRSAD] == "SOL") } { if { $array(HA_FILE_SOL_SAD) == "" } { WarningMessage "NOT SET: SOL file for sites" return 0 } } } } #--- shelx checks if { ([GetValue $arrayname EP_MODE] == "SAD")} { if { ([GetValue $arrayname RUNSHELXD] == "1")} { if { ([GetValue $arrayname HYSS_TYPE] == "")} { WarningMessage "NOT SET: ShelxD atom type" return 0 } } } if { ([GetValue $arrayname EP_MODE] == "SAD")} { if { ([GetValue $arrayname RUNSHELXD] == "1")} { if { ([GetValue $arrayname N_HYSS] == "")} { WarningMessage "NOT SET: Number of sites to find" return 0 } } } if { ([GetValue $arrayname EP_MODE] == "SAD")} { if { ([GetValue $arrayname RUNHYSS] == "1")} { if { ([GetValue $arrayname N_HYSS] == "")} { WarningMessage "NOT SET: Number of sites to find" return 0 } if { ([GetValue $arrayname HYSS_TYPE] == "")} { WarningMessage "NOT SET: Atom type for hyss" return 0 } } } #Define atoms ----partial structure checks if { ([GetValue $arrayname EP_MODE] == "MRSAD") } { if { ([GetValue $arrayname PART_PDB_MTZ] == "PDB")} { if { ([GetValue $arrayname PARTPDB] == "")} { WarningMessage "NOT SET: Partial PDB file" return 0 } } if { ([GetValue $arrayname PART_PDB_MTZ] == "MTZ")} { if { ([GetValue $arrayname PARTMTZ] == "")} { WarningMessage "NOT SET: Partial MTZ file" return 0 } } if { ([GetValue $arrayname PARTIAL_RMSID_OPTION] == "IDENT")} { if { ([GetValue $arrayname PARTIAL_RMSID] == "")} { WarningMessage "NOT SET: sequence identity for the partial structure" return 0 } } if { ([GetValue $arrayname PARTIAL_RMSID_OPTION] == "RMS")} { if { ([GetValue $arrayname PARTIAL_RMSID] == "")} { WarningMessage "NOT SET: rms difference for the partial structure" return 0 } } } #----Cluster checks if { ([GetValue $arrayname EP_MODE] == "SAD") } { if { ([GetValue $arrayname TOG_CLUSTER] == "1") } { if { ([GetValue $arrayname CLUSTER_FILE_PDB] == "") } { WarningMessage "NOT SET: Cluster PDB file" return 0 } } } if { ([GetValue $arrayname EP_MODE] == "MRSAD") } { if { ([GetValue $arrayname TOG_CLUSTER_MR] == "1") } { if { ([GetValue $arrayname CLUSTER_FILE_PDB_MR] == "") } { WarningMessage "NOT SET: Cluster PDB file" return 0 } } } #Define atoms ---- LLG completion checks if { ([GetValue $arrayname TOG_LLGC_SAD] == "1") } { if { ([GetValue $arrayname LLGC_COMPLETE_SAD] == "ON") } { if { ([GetValue $arrayname EP_MODE] == "MRSAD") } { if { ([GetValue $arrayname TOG_LLGC_SAD_ATOM] == "0") && ([GetValue $arrayname TOG_LLGC_SAD_ANOM] == "0") && ([GetValue $arrayname TOG_LLGC_SAD_REAL] == "0") } { WarningMessage "NOT SET: Completion method" return 0 } } } } if { ([GetValue $arrayname TOG_LLGC_SAD] == "1") } { if { ([GetValue $arrayname LLGC_COMPLETE_SAD] == "ON") } { if { ([GetValue $arrayname TOG_LLGC_SAD_ATOM] == "1") } { if { ([GetValue $arrayname LLGC_FIRST_TYPE] == "") } { WarningMessage "NOT SET: Completion atom type (array empty)" return 0 } for { set n 1 } { $n <= $array(N_LLGC) } { incr n } { if { ($array(LLGC_TYPE,$n) == "") } { WarningMessage "NOT SET: Completion atom type" return 0 } } } } } #Hyss and Shelx folder if { ([GetValue $arrayname HA_SITES_OPTION_SAD] == "HYSS") } { if { ([GetValue $arrayname TOG_HYSS_SOLVENT] == "1") } { if { ([GetValue $arrayname SCATTERING_SOLVENT] == "") } { WarningMessage "NOT SET: solvent content in for phenix.hyss" return 0 } } } if { ([GetValue $arrayname HA_SITES_OPTION_SAD] == "SHELXD") } { if { ([GetValue $arrayname TOG_NTRY] == "1") && ([GetValue $arrayname NTRY] == "") } { WarningMessage "NOT SET: Number of trys for SHELXD" return 0 } } if { ([GetValue $arrayname HA_SITES_OPTION_SAD] == "HYSS") || ([GetValue $arrayname HA_SITES_OPTION_SAD] == "SHELXD") } { if { ([GetValue $arrayname TOG_MIND] == "1") && ([GetValue $arrayname MIND] == "") } { WarningMessage "NOT SET: minimum distance between heavy atoms" return 0 } if { ([GetValue $arrayname TOG_SHELXC_RESO] == "1") && ([GetValue $arrayname MIN_RESO] == "") } { WarningMessage "NOT SET: resolution for heavy atom search" return 0 } if { ([GetValue $arrayname TOG_SHELXC_RESO] == "1") && ([GetValue $arrayname MAX_RESO] == "") } { WarningMessage "NOT SET: resolution for heavy atom search" return 0 } } # Composition of the ASU if { ([GetValue $arrayname SCATTERING] == "ASU") } { 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 } } 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 } } } # Accessory Parameters if { ([GetValue $arrayname TOG_SCAT_RESTRAIN] == "1") } { if { ([GetValue $arrayname SCAT_RESTRAIN] == "ON") } { if { ([GetValue $arrayname SCAT_SIGMA] == "") } { WarningMessage "NOT SET: No Sigma for scattering restraint" } } } # Files set array(INPUT_FILES) "HKLIN" if {([GetValue $arrayname EP_MODE] == "SAD") } { if {([GetValue $arrayname HA_SITES_OPTION_SAD] == "HA") && ([GetValue $arrayname HA_FILE_HA_SAD] != "") } { append array(INPUT_FILES) " HA_FILE_HA_SAD" } if {([GetValue $arrayname HA_SITES_OPTION_SAD] == "SOL") && ([GetValue $arrayname HA_FILE_SOL_SAD] != "") } { append array(INPUT_FILES) " HA_FILE_SOL_SAD" } if {([GetValue $arrayname HA_SITES_OPTION_SAD] == "PDB") && ([GetValue $arrayname HA_FILE_PDB_SAD] != "") } { append array(INPUT_FILES) " HA_FILE_PDB_SAD" } if { ([GetValue $arrayname TOG_CLUSTER] == "1") && ([GetValue $arrayname CLUSTER_FILE_PDB] != "") } { append array(INPUT_FILES) " CLUSTER_FILE_PDB" } } if {([GetValue $arrayname EP_MODE] == "MRSAD") } { if {([GetValue $arrayname PART_PDB_MTZ] == "PDB") && ([GetValue $arrayname PARTPDB] != "") } { append array(INPUT_FILES) " PARTPDB" } if {([GetValue $arrayname PART_PDB_MTZ] == "MTZ") && ([GetValue $arrayname PARTMTZ] != "") } { append array(INPUT_FILES) " PARTMTZ" } if {([GetValue $arrayname HA_SITES_OPTION_MRSAD] == "HA") && ([GetValue $arrayname HA_FILE_HA_SAD] != "") } { append array(INPUT_FILES) " HA_FILE_HA_SAD" } if {([GetValue $arrayname HA_SITES_OPTION_MRSAD] == "SOL") && ([GetValue $arrayname HA_FILE_SOL_SAD] != "") } { append array(INPUT_FILES) " HA_FILE_SOL_SAD" } if {([GetValue $arrayname HA_SITES_OPTION_MRSAD] == "PDB") && ([GetValue $arrayname HA_FILE_PDB_SAD] != "") } { append array(INPUT_FILES) " HA_FILE_PDB_SAD" } if { ([GetValue $arrayname TOG_CLUSTER_MR] == "1") && ([GetValue $arrayname CLUSTER_FILE_PDB_MR] == "") } { append array(INPUT_FILES) " CLUSTER_FILE_PDB_MR" } } 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 { ![SetHarvestParams $arrayname HKLIN -run] } { return 0 } if { ([GetValue $arrayname RUNBUCCANEER] == "1") || ([GetValue $arrayname RUNPARROT] == "1") } { if { ([GetValue $arrayname SCATTERING] != "COMPONENT") } { WarningMessage "NOT SET: sequence file for parrot/buccaneer\nEnter sequence" return 0 } } if { ([GetValue $arrayname RUNBUCCANEER] == "1") || ([GetValue $arrayname RUNPARROT] == "1") } { if { ($array(COMP_OPTION,1) != "sequence file")} { WarningMessage "NOT SET: sequence file for parrot/buccaneer\nEnter composition by sequence" return 0 } if { ($array(COMP_FILE,1) == "") } { WarningMessage "NOT SET: sequence file for parrot/buccaneer\nEnter sequence" return 0 } } # All output files with the user specified root will be saved to the project dir return 1 } #------------------------------------------------------------------------ proc phaser_EP_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_EP_atomsearch { arrayname } { #------------------------------------------------------------------------ upvar #0 $arrayname array if { [GetValue $arrayname ATOMSEARCH] == "SHELXD" && [GetValue $arrayname TOG_ATOMSEARCH] == "1" } { set array(HA_SITES_OPTION_SAD) "run ShelxC/D" } elseif { [GetValue $arrayname ATOMSEARCH] == "HYSS" && [GetValue $arrayname TOG_ATOMSEARCH] == "1" } { set array(HA_SITES_OPTION_SAD) "run phenix.hyss" } elseif { [GetValue $arrayname TOG_ATOMSEARCH] == "0" } { set array(HA_SITES_OPTION_SAD) "in PDB file" } if { [GetValue $arrayname HYSS_INSTALLED] == "1" && \ [GetValue $arrayname ATOMSEARCH] == "HYSS" && \ [GetValue $arrayname EP_MODE] == "SAD" } { set array(SHOW_HYSS) 1 } else { set array(SHOW_HYSS) 0 } if { [GetValue $arrayname SHELXD_INSTALLED] == "1" && \ [GetValue $arrayname ATOMSEARCH] == "SHELXD" && \ [GetValue $arrayname EP_MODE] == "SAD" } { set array(SHOW_SHELX) 1 } else { set array(SHOW_SHELX) 0 } } #------------------------------------------------------------------------ proc phaser_EP_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_EP_dwave { arrayname } { #--------------------------------------------------------------------- # # Get cell information based on HKLIN and F label upvar \#0 $arrayname array # Acquire actual values of task parameters set filen [GetFullFileName0 $arrayname HKLIN] set label [GetValue $arrayname "Fp_SAD"] # Extract xtal and dataset names, given filename and a column name if { ![GetMtzDatasetFromLabel $filen $label xtal dataset] } { return 0 } # Get crystal cell for the specific crystal/dataset if { ![GetMtzParamFromDataset $filen $xtal $dataset DWAVES dwave] } { return 0 } set array(WAVELENGTH) $dwave set_field_colour $arrayname WAVELENGTH 1 return } #------------------------------------------------------------------------ proc phaser_EP_ha { arrayname counter_a } { #------------------------------------------------------------------------ # Procedure to define a anomalous atom site manually upvar #0 $arrayname array CreateLine line \ message "Add new atom site manually" \ widget HA_ATOM_TYPE_SAD -oblig -width 30 \ widget HA_ATOM_FRAC_SAD \ widget HA_ATOM_X_SAD -oblig \ widget HA_ATOM_Y_SAD -oblig \ widget HA_ATOM_Z_SAD -oblig \ widget HA_ATOM_O_SAD -oblig \ widget HA_ATOM_B_SAD } #------------------------------------------------------------------------ proc phaser_EP_hamr { arrayname counter_a } { #------------------------------------------------------------------------ # Procedure to define a anomalous atom site manually upvar #0 $arrayname array CreateLine line \ message "Add new atom site manually" \ widget HA_ATOM_TYPE_MRSAD -oblig -width 30 \ widget HA_ATOM_FRAC_MRSAD \ widget HA_ATOM_X_MRSAD -oblig \ widget HA_ATOM_Y_MRSAD -oblig \ widget HA_ATOM_Z_MRSAD -oblig \ widget HA_ATOM_O_MRSAD -oblig \ widget HA_ATOM_B_MRSAD } #------------------------------------------------------------------------ proc phaser_EP_llgc { arrayname counter_f } { #------------------------------------------------------------------------ # Procedure to define a scattering for atom manually upvar #0 $arrayname array CreateLineTemplate BB { 0 0.2 0.45 } CreateLine line \ message "Atomtypes for LLG-maps" \ label "" label "or with atom type" \ widget LLGC_TYPE \ -command "phaser_EP_llgc_sad_toggle_update $arrayname " \ format template BB } #------------------------------------------------------------------------ proc phaser_EP_maca { arrayname counter_s } { #------------------------------------------------------------------------ global configure upvar #0 $arrayname array CreateLine line \ label "Refine: 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 } #------------------------------------------------------------------------ proc phaser_EP_macs { arrayname counter_s } { #------------------------------------------------------------------------ global configure upvar #0 $arrayname array CreateLine line \ message "Overall Occupancy Scale" \ widget TOG_MACSAD_K \ message "Overall B-factor" \ widget TOG_MACSAD_B \ message "Overall Sigma Scale" \ widget TOG_MACSAD_SIGMA \ message "Atom positions" \ widget TOG_MACSAD_XYZ \ message "Atom occupancy" \ widget TOG_MACSAD_OCC \ message "Atom B-factor" \ widget TOG_MACSAD_BFAC \ message "Atom F double prime" \ widget TOG_MACSAD_FDP \ message "Variance Real part of D-phi" \ widget TOG_MACSAD_SA \ message "Variance Imaginary part of D-phi" \ widget TOG_MACSAD_SB \ message "Variance Sigma-Plus" \ widget TOG_MACSAD_SP \ message "Variance Sigma-Delta" \ widget TOG_MACSAD_SD \ message "Number of Cycles" \ widget MACSAD_NCYCL \ format template MACSAD_TEMPLATE } #------------------------------------------------------------------------ proc phaser_EP_macs_part { arrayname counter_s } { #------------------------------------------------------------------------ global configure upvar #0 $arrayname array CreateLine line \ message "Overall Occupancy Scale" \ widget TOG_MACSAD_K \ message "Overall B-factor" \ widget TOG_MACSAD_B \ message "Overall Sigma Scale" \ widget TOG_MACSAD_SIGMA \ message "Atom positions" \ widget TOG_MACSAD_XYZ \ message "Atom occupancy" \ widget TOG_MACSAD_OCC \ message "Atom B-factor" \ widget TOG_MACSAD_BFAC \ message "Atom F double prime" \ widget TOG_MACSAD_FDP \ message "Variance Real part of D-phi" \ widget TOG_MACSAD_SA \ message "Variance Imaginary part of D-phi" \ widget TOG_MACSAD_SB \ message "Variance Sigma-Plus" \ widget TOG_MACSAD_SP \ message "Variance Sigma-Delta" \ widget TOG_MACSAD_SD \ message "Partial Structure Scale" \ widget TOG_MACSAD_PK \ message "Partial Structure B-factor" \ widget TOG_MACSAD_PB \ message "Number of Cycles" \ widget MACSAD_NCYCL \ format template MACSAD_PART_TEMPLATE } #------------------------------------------------------------------------ proc phaser_EP_show_labin_F { arrayname } { #------------------------------------------------------------------------ upvar #0 $arrayname array set array(LABIN_F) 0 if { [GetValue $arrayname RUNBUCCANEER] == "1" || [GetValue $arrayname EP_SAMR] == "1" } { set array(LABIN_F) 1 } } #------------------------------------------------------------------------ proc phaser_EP_mode_update { arrayname } { #------------------------------------------------------------------------ upvar #0 $arrayname array if { [GetValue $arrayname EP_MODE] == "SAD" } { set array(TOG_ADDITIONAL_ATOMS) 0 } elseif { [GetValue $arrayname EP_MODE] == "MRSAD" && [GetValue $arrayname TOG_ADDITIONAL_ATOMS_BAK] == "1"} { set array(TOG_ADDITIONAL_ATOMS) 1 } elseif { [GetValue $arrayname EP_MODE] == "MRSAD" && [GetValue $arrayname TOG_ADDITIONAL_ATOMS_BAK] == "0"} { set array(TOG_ADDITIONAL_ATOMS) 0 } if { [GetValue $arrayname EP_MODE] == "SAD" && [GetValue $arrayname TOG_LLGC_SAD] == "0" } { set array(LLGC_COMPLETE_SAD) "on: all atom types" } elseif { [GetValue $arrayname EP_MODE] == "MRSAD" && [GetValue $arrayname TOG_LLGC_SAD] == "0" } { set array(LLGC_COMPLETE_SAD) "on: select atom types" } if { [GetValue $arrayname HYSS_INSTALLED] == "1" && \ [GetValue $arrayname HA_SITES_OPTION_SAD] == "HYSS" && \ [GetValue $arrayname EP_MODE] == "SAD" } { set array(SHOW_HYSS) 1 } else { set array(SHOW_HYSS) 0 } if { [GetValue $arrayname SHELXD_INSTALLED] == "1" && \ [GetValue $arrayname HA_SITES_OPTION_SAD] == "SHELXD" && \ [GetValue $arrayname EP_MODE] == "SAD" } { set array(SHOW_SHELX) 1 } else { set array(SHOW_SHELX) 0 } if { [GetValue $arrayname HA_SITES_OPTION_SAD] == "HYSS" } { set array(TOG_ATOMSEARCH) 1 set array(ATOMSEARCH) "HYSS" } elseif { [GetValue $arrayname HA_SITES_OPTION_SAD] == "SHELXD" } { set array(TOG_ATOMSEARCH) 1 set array(ATOMSEARCH) "SHELXD" } else { set array(TOG_ATOMSEARCH) 0 } } #------------------------------------------------------------------------ proc phaser_EP_atom_toggle_update { arrayname } { #------------------------------------------------------------------------ upvar #0 $arrayname array if { [GetValue $arrayname TOG_ADDITIONAL_ATOMS] == "1"} { set array(TOG_ADDITIONAL_ATOMS_BAK) 1 } elseif { [GetValue $arrayname TOG_ADDITIONAL_ATOMS] == "0"} { set array(TOG_ADDITIONAL_ATOMS_BAK) 0 } if { [GetValue $arrayname HYSS_INSTALLED] == "1" && \ [GetValue $arrayname HA_SITES_OPTION_SAD] == "HYSS" && \ [GetValue $arrayname EP_MODE] == "SAD" } { set array(SHOW_HYSS) 1 } else { set array(SHOW_HYSS) 0 } if { [GetValue $arrayname SHELXD_INSTALLED] == "1" && \ [GetValue $arrayname HA_SITES_OPTION_SAD] == "SHELXD" && \ [GetValue $arrayname EP_MODE] == "SAD" } { set array(SHOW_SHELX) 1 } else { set array(SHOW_SHELX) 0 } if { [GetValue $arrayname HA_SITES_OPTION_SAD] == "HYSS" && [GetValue $arrayname HYSS_INSTALLED] == "1" } { set array(TOG_ATOMSEARCH) 1 set array(ATOMSEARCH) HYSS } elseif { [GetValue $arrayname HA_SITES_OPTION_SAD] == "SHELXD" && [GetValue $arrayname SHELXD_INSTALLED] == "1" } { set array(TOG_ATOMSEARCH) 1 set array(ATOMSEARCH) SHELXD } else { set array(TOG_ATOMSEARCH) 0 } } #------------------------------------------------------------------------ proc phaser_EP_reso_toggle_update { arrayname } { #------------------------------------------------------------------------ upvar #0 $arrayname array set array(TOG_RESOLUTION) 1 if { [GetValue $arrayname RESOLUTION_DMAX] == ""} { set array(TOG_RESOLUTION) 0 } if { [GetValue $arrayname RESOLUTION_DMIN] == ""} { set array(TOG_RESOLUTION) 0 } } #------------------------------------------------------------------------ proc phaser_EP_llgc_toggle_update { arrayname } { #------------------------------------------------------------------------ upvar #0 $arrayname array if { [GetValue $arrayname TOG_LLGC_SAD] == "0" } { set array(TOG_LLGC_SAD_ATOM) 0 set array(TOG_LLGC_SAD_ANOM) 0 set array(TOG_LLGC_SAD_REAL) 0 } } #------------------------------------------------------------------------ proc phaser_EP_llgc_sad_toggle_update { arrayname } { #------------------------------------------------------------------------ upvar #0 $arrayname array set array(TOG_LLGC_SAD) 0 if { [GetValue $arrayname TOG_LLGC_SAD_ATOM] == "1" } { set array(TOG_LLGC_SAD) 1 } if { [GetValue $arrayname TOG_LLGC_SAD_REAL] == "1" } { set array(TOG_LLGC_SAD) 1 } if { [GetValue $arrayname TOG_LLGC_SAD_ANOM] == "1" } { set array(TOG_LLGC_SAD) 1 } for { set n 1 } { $n <= $array(N_LLGC) } { incr n } { if { !($array(LLGC_TYPE,$n) == "") } { set array(TOG_LLGC_SAD) 1 set array(TOG_LLGC_SAD_ATOM) 1 } } } #------------------------------------------------------------------------ proc phaser_EP_task_window {arrayname} { #------------------------------------------------------------------------ upvar #0 $arrayname array global configure if { [CreateTaskWindow $arrayname \ "Maximum Likelihood Experimental Phasing"\ "Phaser" \ [ list "Define data" \ "Define atoms" \ "phenix.hyss parameters" \ "Shelx parameters" \ "Composition of the asymmetric unit" \ "Accessory parameters" \ "Output control" \ "Expert parameters" ] \ ] == 0 } return SetHarvestParams $arrayname HKLIN -init if { ![file exists [FindExecutable phenix.hyss]] } { set array(HYSS_INSTALLED) "0" } if { ![file exists [FindExecutable mtz2sca]] } { set array(SHELXD_INSTALLED) "0" } if { ![file exists [FindExecutable shelxc]] } { set array(SHELXD_INSTALLED) "0" } if { ![file exists [FindExecutable shelxd]] } { set array(SHELXD_INSTALLED) "0" } if { ![file exists [FindExecutable shelxd]] && ![file exists [FindExecutable phenix.hyss]] } { set array(ATOMSEARCH_INSTALLED) "0" } if { ![file exists [FindExecutable shelxd]] || ![file exists [FindExecutable phenix.hyss]] } { set array(ATOMSEARCH_BOTH_INSTALLED) "0" } if { [GetValue $arrayname SHELXD_INSTALLED] == "1" && [GetValue $arrayname HYSS_INSTALLED] == "0" } { set array(ATOMSEARCH) "SHELXD" } if { [GetValue $arrayname SHELXD_INSTALLED] == "0" && [GetValue $arrayname HYSS_INSTALLED] == "1" } { set array(ATOMSEARCH) "HYSS" } if { [GetValue $arrayname ATOMSEARCH_INSTALLED] == "1" && \ [GetValue $arrayname TOG_ATOMSEARCH] == "1" && \ [GetValue $arrayname SHELXD_INSTALLED] == "1" && \ [GetValue $arrayname ATOMSEARCH] == "SHELXD" } { set array(HA_SITES_OPTION_SAD) "run ShelxC/D" } if { [GetValue $arrayname ATOMSEARCH_INSTALLED] == "1" && \ [GetValue $arrayname TOG_ATOMSEARCH] == "1" && \ [GetValue $arrayname HYSS_INSTALLED] == "1" && \ [GetValue $arrayname ATOMSEARCH] == "HYSS" } { set array(HA_SITES_OPTION_SAD) "run phenix.hyss" } if { [GetValue $arrayname HYSS_INSTALLED] == "1" && \ [GetValue $arrayname HA_SITES_OPTION_SAD] == "HYSS" && \ [GetValue $arrayname EP_MODE] == "SAD" } { set array(SHOW_HYSS) 1 } else { set array(SHOW_HYSS) 0 } if { [GetValue $arrayname SHELXD_INSTALLED] == "1" && \ [GetValue $arrayname HA_SITES_OPTION_SAD] == "SHELXD" && \ [GetValue $arrayname EP_MODE] == "SAD" } { set array(SHOW_SHELX) 1 } else { set array(SHOW_SHELX) 0 } # SetProgramHelpFile phaser #=PROTOCOL=============================================================== OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ label "Mode for experimental phasing" \ widget EP_MODE \ -command "phaser_EP_mode_update $arrayname " CreateLine line \ label "Phaser SAD pipeline" -italic OpenSubFrame frame -toggle_display EP_MODE open SAD hide MRSAD OpenSubFrame frame -toggle_display ATOMSEARCH_INSTALLED open 1 hide CreateLine line \ message "Run Heavy Atom Location before Phaser SAD" \ widget TOG_ATOMSEARCH -toggleon -width 4 \ -command "phaser_EP_atomsearch $arrayname " \ label "Run " \ widget ATOMSEARCH -command "phaser_EP_atomsearch $arrayname " \ label " before Phaser" \ toggle_display ATOMSEARCH_BOTH_INSTALLED open 1 hide OpenSubFrame frame -toggle_display ATOMSEARCH_BOTH_INSTALLED open 0 hide CreateLine line \ message "Run Heavy Atom Location before Phaser SAD" \ widget TOG_ATOMSEARCH -toggleon -width 4 \ -command "phaser_EP_atomsearch $arrayname " \ label "Run " \ widget ATOMSEARCH -command "phaser_EP_atomsearch $arrayname " \ label " before Phaser" \ label " mtz2sca/shelxc/shelxd are not installed or path not set" -italic \ toggle_display SHELXD_INSTALLED open 0 hide CreateLine line \ message "Run Heavy Atom Location before Phaser SAD" \ widget TOG_ATOMSEARCH -toggleon -width 4 \ -command "phaser_EP_atomsearch $arrayname " \ label "Run " \ widget ATOMSEARCH -command "phaser_EP_atomsearch $arrayname" \ label " before Phaser" \ label " phenix.hyss is not installed or path not set" -italic \ toggle_display HYSS_INSTALLED open 0 hide CloseSubFrame CloseSubFrame CloseSubFrame CreateLine line \ message "Run Density Modification and Model Building after Phaser SAD" \ widget RUNPARROT -width 4 \ label "Run Parrot (density modification) after Phaser" \ widget RUNBUCCANEER -width 4 \ -command "phaser_EP_show_labin_F $arrayname" \ label "Run Buccaneer (model building) after Parrot" #======================================================================== # The "Define data" folder OpenFolder 1 CreateInputFileLine line \ "Enter MTZ file name (HKLIN)" \ "MTZ in " \ HKLIN DIR_HKLIN \ -setfileparam resolution_min RESOLUTION_DMAX \ -setfileparam resolution_max RESOLUTION_DMIN \ -setfileparam resolution_min MIN_RESO \ -setfileparam resolution_max MAX_RESO \ -setfileparam space_group_name FILE_SPACEGROUP \ -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 \ -setlabin Fp_SAD [list "*+*" ] \ -setlabin SIGFp_SAD [list "*+*"] \ -setlabin Fn_SAD [list "*-*"] \ -setlabin SIGFn_SAD [list "*-*"] \ -setlabin FPwrk {} \ -setlabin SIGFPwrk [list SIGF "*SIG*"] \ -setlabin FREE [list FREER FreeR FreeR_flag] \ -command "UpdateHarvestMTZ $arrayname HKLIN" \ -command "phaser_EP_dwave $arrayname" CreateHarvestLine line -noharv OpenSubFrame frame -toggle_display EP_SAMR open 0 hide CreateLabinLine line \ "Select anomalous amplitude F+ and anomalous sigma SIGF+" \ HKLIN "F(+)" Fp_SAD [list "*+*" ] \ -sigma "SIGF(+)" SIGFp_SAD [list "*+*"] \ -command "phaser_EP_dwave $arrayname" CreateLabinLine line \ "Select anomalous amplitude F- and anomalous sigma SIGF-" \ HKLIN "F(-)" Fn_SAD [list "*-*"] \ -sigma "SIGF(-)" SIGFn_SAD [list "*-*"] CloseSubFrame OpenSubFrame frame -toggle_display LABIN_F open 1 hide CreateLabinLine line \ "Observed amplitude (FP) and sigma (SIGFP)" \ HKLIN "FP" FPwrk {} \ -sigma "SIGFP" SIGFPwrk [list SIGF "*SIG*"] CreateLabinLine line \ "Free R flags" \ HKLIN "FREER" FREER {} \ CloseSubFrame CreateLine line \ message "Default is to take all data" \ widget TOG_RESOLUTION \ label "Resolution" widget RESOLUTION_DMAX -command "phaser_EP_reso_toggle_update $arrayname" \ label "A to" widget RESOLUTION_DMIN -command "phaser_EP_reso_toggle_update $arrayname" \ label "A; " \ message "Wavelength of the SAD data" \ label "Wavelength" \ widget WAVELENGTH -oblig CreateLine line \ message "Space group read from mtz file." \ label "Space group read from mtz file" \ varlabel FILE_SPACEGROUP \ toggle_display EP_MODE open MRSAD hide SAD CreateLine line \ message "Space group read from mtz file." \ label "Space group read from mtz file" \ varlabel FILE_SPACEGROUP \ label ";" \ message "Keep or change enantiomorph of input sites" \ widget TOG_HAND_OPTION -toggleon label "Enantiomorph choice" widget HAND_ONOFF \ toggle_display EP_MODE open SAD hide MRSAD CreateLine line \ widget TOG_SCAT_MEASURED \ label "Enter scattering from fluorescence scan (default is to calculate f' and f\" from wavelength)" CreateLine line \ message "Enter measured f' and f''" \ label "type" widget SCAT_TYPE -oblig \ label "FP =" widget SCAT_FP -oblig \ label "FDP =" widget SCAT_FDP -oblig \ message "Phaser will determine if near edge" \ label "Refine Fdp" widget SCAT_REF \ toggle_display TOG_SCAT_MEASURED open 1 hide #======================================================================== # The "Define atoms " folder OpenFolder 2 OpenSubFrame frame -toggle_display EP_MODE open MRSAD hide CreateLine line \ label "Partial structure input as" \ widget PART_PDB_MTZ \ label "file (real scattering only)" CreateInputFileLine line \ "Select a PDB file for starting partial structure" \ "PDB in " \ PARTPDB DIR_PARTPDB \ -toggle_display PART_PDB_MTZ open PDB hide CreateInputFileLine line \ "Select a MTZ file for starting partial structure" \ "MTZ in " \ PARTMTZ DIR_PARTMTZ \ -toggle_display PART_PDB_MTZ open MTZ hide CreateLine line \ message "Specify RMS error in Angstrom, or \ via the sequence identity (percentage or a fraction)" \ label "Similarity of partial structure to the target structure" \ widget PARTIAL_RMSID_OPTION \ widget PARTIAL_RMSID -oblig \ toggle_display EP_MODE open MRSAD hide CreateLine line \ widget TOG_ADDITIONAL_ATOMS -command "phaser_EP_atom_toggle_update $arrayname" \ label "Positions of (some) anomalous scatterers are known" CloseSubFrame # Define the scattering atoms long form================= OpenSubFrame frame -toggle_display EP_MODE open SAD hide CreateLine line \ message "Select how you wish to define the atom sites" \ label "Atom sites" widget HA_SITES_OPTION_SAD -command "phaser_EP_mode_update $arrayname" \ toggle_display HA_SITES_OPTION_SAD open [list PDB SOL HA MANUAL] hide OpenSubFrame frame -toggle_display HA_SITES_OPTION_SAD open HYSS hide CreateLine line \ message "Select how you wish to define the atom sites" \ label "Atom sites" widget HA_SITES_OPTION_SAD -command "phaser_EP_mode_update $arrayname" \ toggle_display HYSS_INSTALLED open 1 hide CreateLine line \ message "Select how you wish to define the atom sites" \ label "Atom sites" widget HA_SITES_OPTION_SAD -command "phaser_EP_mode_update $arrayname" \ label "phenix.hyss is not installed or path not set" -italic \ toggle_display HYSS_INSTALLED open 0 hide CloseSubFrame OpenSubFrame frame -toggle_display HA_SITES_OPTION_SAD open SHELXD hide CreateLine line \ message "Select how you wish to define the atom sites" \ label "Atom sites" widget HA_SITES_OPTION_SAD -command "phaser_EP_atom_toggle_update $arrayname" \ toggle_display SHELXD_INSTALLED open 1 hide CreateLine line \ message "Select how you wish to define the atom sites" \ label "Atom sites" widget HA_SITES_OPTION_SAD -command "phaser_EP_atom_toggle_update $arrayname" \ label "mtz2sca/shelxc/shelxd are not installed or path not set" -italic \ toggle_display SHELXD_INSTALLED open 0 hide CloseSubFrame CreateLine line \ label "Find" widget N_HYSS -oblig \ label "heavy atoms of type" widget HYSS_TYPE -oblig \ toggle_display HA_SITES_OPTION_SAD open [list HYSS ] hide CreateLine line \ label "Find" widget N_HYSS -oblig \ label "heavy atoms of type " widget HYSS_TYPE -oblig \ toggle_display HA_SITES_OPTION_SAD open [list SHELXD] hide CreateInputFileLine line \ "Select the pdb file" "PDB in" HA_FILE_PDB_SAD DIR_HA_FILE_PDB_SAD \ -toggle_display HA_SITES_OPTION_SAD open PDB hide CreateInputFileLine line \ "Select the heavy atom file" "HA in" HA_FILE_HA_SAD DIR_HA_FILE_HA_SAD \ -toggle_display HA_SITES_OPTION_SAD open HA hide CreateInputFileLine line \ "Select the sol file" "SOL in" HA_FILE_SOL_SAD DIR_HA_FILE_SOL_SAD \ -toggle_display HA_SITES_OPTION_SAD open SOL hide OpenSubFrame frame -toggle_display HA_SITES_OPTION_SAD open MANUAL hide CreateLineTemplate HA { 0.0 0.37 0.56 0.65 0.74 0.83 0.92 } CreateLine line \ label "Atom (or Cluster or Real/Anom)" label "Frac/Orth" label "X" label "Y" label "Z" label "O" label "B" \ format template HA CreateExtendingFrame N_HA_SAD phaser_EP_ha \ "Add another atom site" "Add another atom site" \ [list HA_ATOM_TYPE_SAD HA_ATOM_FRAC_SAD HA_ATOM_X_SAD HA_ATOM_Y_SAD HA_ATOM_Z_SAD HA_ATOM_O_SAD HA_ATOM_B_SAD ] CloseSubFrame OpenSubFrame frame -toggle_display HA_SITES_OPTION_SAD open [list SHELXD] hide CloseSubFrame CreateLine line \ widget TOG_CLUSTER \ label "Crystal contains cluster compound" OpenSubFrame frame -toggle_display TOG_CLUSTER open 1 hide CreateInputFileLine line \ "Select the pdb file" "PDB in" CLUSTER_FILE_PDB DIR_CLUSTER_FILE_PDB CloseSubFrame CloseSubFrame # define the scattering atoms short form (no hyss or shelxd) ============ OpenSubFrame frame -toggle_display TOG_ADDITIONAL_ATOMS open 1 hide CreateLine line \ message "Select how you wish to define the atom sites" \ label "Atom sites" widget HA_SITES_OPTION_MRSAD \ toggle_display HA_SITES_OPTION_MRSAD open [list PDB SOL HA MANUAL] hide CreateInputFileLine line \ "Select the pdb file" "PDB in" HA_FILE_PDB_SAD DIR_HA_FILE_PDB_SAD \ -toggle_display HA_SITES_OPTION_MRSAD open PDB hide CreateInputFileLine line \ "Select the heavy atom file" "HA in" HA_FILE_HA_SAD DIR_HA_FILE_HA_SAD \ -toggle_display HA_SITES_OPTION_MRSAD open HA hide CreateInputFileLine line \ "Select the sol file" "SOL in" HA_FILE_SOL_SAD DIR_HA_FILE_SOL_SAD \ -toggle_display HA_SITES_OPTION_MRSAD open SOL hide OpenSubFrame frame -toggle_display HA_SITES_OPTION_MRSAD open MANUAL hide CreateLineTemplate HASAD { 0.0 0.37 0.56 0.65 0.74 0.83 0.92 } CreateLine line \ label "Atom (or Cluster or Real/Anom)" label "Frac/Orth" label "X" label "Y" label "Z" label "O" label "B" \ format template HASAD CreateExtendingFrame N_HA_MRSAD phaser_EP_hamr \ "Add another atom site" "Add another atom site" \ [list HA_ATOM_TYPE_MRSAD HA_ATOM_FRAC_MRSAD HA_ATOM_X_MRSAD HA_ATOM_Y_MRSAD HA_ATOM_Z_MRSAD HA_ATOM_O_MRSAD HA_ATOM_B_MRSAD ] CloseSubFrame CreateLine line \ widget TOG_CLUSTER_MR \ label "Crystal contains cluster compound (coordinates in pdb file below)" OpenSubFrame frame -toggle_display TOG_CLUSTER_MR open 1 hide CreateInputFileLine line \ "Select the pdb file" "PDB in" CLUSTER_FILE_PDB_MR DIR_CLUSTER_FILE_PDB_MR CloseSubFrame CloseSubFrame CreateLine line \ widget TOG_LLGC_SAD -toggleon -command "phaser_EP_llgc_toggle_update $arrayname" \ label "LLG-map completion" \ widget LLGC_COMPLETE_SAD CreateLine line \ label " " \ widget TOG_LLGC_SAD_REAL -toggleon -command "phaser_EP_llgc_sad_toggle_update $arrayname" \ label "Complete with purely real scatterer" \ toggle_display LLGC_COMPLETE_SAD open ON hide CreateLine line \ label " " \ widget TOG_LLGC_SAD_ANOM -toggleon -command "phaser_EP_llgc_sad_toggle_update $arrayname" \ label "Complete with purely anomalous scatterer" \ toggle_display LLGC_COMPLETE_SAD open ON hide CreateLine line \ label " " \ widget TOG_LLGC_SAD_ATOM -toggleon -command "phaser_EP_llgc_sad_toggle_update $arrayname" \ label "Complete with atom type " \ widget LLGC_FIRST_TYPE \ toggle_display LLGC_COMPLETE_SAD open ON hide OpenSubFrame frame -toggle_display LLGC_COMPLETE_SAD open ON hide CreateExtendingFrame N_LLGC phaser_EP_llgc \ "Add another atomtype" "Add another atomtype" \ [list LLGC_TYPE ] CloseSubFrame #======================================================================== # The "phenix.hyss parameters" of the asymmetric unit folder OpenFolder 3 SHOW_HYSS closed 1 hide CreateLine line \ message "Take default cutoffs calculated automatically by phenix.hyss" \ widget TOG_SHELXC_RESO -toggleon \ label "Override default resolution limits: high resolution" \ widget MAX_RESO label "A" CreateLine line \ message "The minimum distance should depend on the type and clustering of the heavy atoms" \ widget TOG_MIND -toggleon \ label "Minimum distance between heavy atoms" \ widget MIND \ label "Angstrom" CreateLine line \ widget TOG_HYSS_SEARCH -toggleon \ label "Search mode" \ widget HYSS_SEARCH CreateLine line \ message "Solvent content (default: 0.55)" \ widget TOG_HYSS_SOLVENT -toggleon \ label "Solvent Content" \ widget SCATTERING_SOLVENT CreateLine line \ message "Useful if substructure location is difficult" \ widget TOG_HYSS_PHASER -toggleon \ label "Use Phaser rescoring in hyss" #======================================================================== # The "Shelx parameters" of the asymmetric unit folder OpenFolder 4 SHOW_SHELX closed 1 hide CreateLine line \ message "Take default cutoffs calculated automatically by SHELXC" \ widget TOG_SHELXC_RESO -toggleon \ label "Override default resolution limits: Use data from" \ widget MIN_RESO label "to" widget MAX_RESO label "A" CreateLine line \ message "Number of attempts at finding atoms (in some cases > 1000 tries may be required)" \ widget TOG_NTRY -toggleon \ label "Limit number of tries to" \ widget NTRY CreateLine line \ message "The minimum distance should depend on the type and clustering of the heavy atoms" \ widget TOG_MIND -toggleon \ label "Minimum distance between heavy atoms" \ widget MIND \ label "Angstrom" CreateLine line \ message "Normally atoms on special positions will be rejected by SHELXD (sets MIND ... -0.1)" \ widget ALLOW_SPECIAL_POS \ label "Allow for heavy atoms lying on special positions" # CreateLine line \ message "Choose whether or not starting atoms should be found from the Patterson" \ widget PATS_ONOFF \ label "Run a Patterson-search to find a starting set of atoms." #======================================================================== # The "Define Composition" of the asymmetric unit folder OpenFolder 5 open CreateLine line \ message "Total scattering of atoms in the asymmetric unit" \ label "Total scattering determined by "\ widget SCATTERING \ toggle_display SCATTERING open [list AVERAGE COMPONENT ] 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_EP_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 #======================================================================== # The "Accessory parameters" folder OpenFolder 6 closed CreateLine line \ widget TOG_SCAT_RESTRAIN -toggleon \ label "Restrain Fdp to starting value" \ widget SCAT_RESTRAIN \ toggle_display SCAT_RESTRAIN open OFF CreateLine line \ widget TOG_SCAT_RESTRAIN -toggleon \ label "Restrain Fdp to starting value" \ widget SCAT_RESTRAIN \ label "Sigma of restraint" \ widget SCAT_SIGMA \ label " (times initial Fdp)" \ toggle_display SCAT_RESTRAIN open ON CreateLine line \ message "Default sigma cut-off = 6" \ widget TOG_LLGC_SAD_SIGMA -toggleon \ label "LLG-map sigma cut-off for adding new atom sites" \ widget LLGC_SIGMA_SAD CreateLine line \ message "Default clash distance is optical resolution" \ widget TOG_LLGC_SAD_CLASH -toggleon \ label "LLG-map atomic separation distance cut-off default" \ widget LLGC_CLASH_DEFAULT \ toggle_display LLGC_CLASH_DEFAULT open ON CreateLine line \ message "Default clash distance is optical resolution" \ widget TOG_LLGC_SAD_CLASH -toggleon \ label "LLG-map atomic separation distance cut-off default" \ widget LLGC_CLASH_DEFAULT \ label "Distance" \ widget LLGC_CLASH_DISTANCE \ toggle_display LLGC_CLASH_DEFAULT open OFF CreateLine line \ widget TOG_LLGC_SAD_NCYC -toggleon \ label "Maximum number of LLG-map completion cycles" \ widget LLGC_NCYC CreateLine line \ widget TOG_LLGC_SAD_METH -toggleon \ label "LLG-map completion picks peaks from " \ widget LLGC_METHOD #======================================================================== # The "Output control" folder OpenFolder 7 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 \ widget TOG_SCRIPT -toggleon \ label "SOL file output" \ widget SCRIPT_ONOFF CreateLine line \ message "Controls output of PDB files containing potential solutions.\ Default depends on mode." \ 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 CreateLine line \ message "Controls output of LLG map coefficients to MTZ file" \ widget TOG_LLGC_SAD_MAPS -toggleon \ label "Output log-likelihood gradient map coefficients" \ widget LLGC_MAPS #======================================================================== # The "Expert parameters" folder OpenFolder 8 closed CreateLine line \ message "Change input atomic B-factors to Wilson" \ widget TOG_CHANGE_BFAC -toggleon \ label "Set B-factors to Wilson B-factor" \ widget CHANGE_BFAC_ONOFF 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_EP_maca \ "Customize the anisotropic refinement" \ "Add another anisotropic macrocycle" \ [list MACA_ANIS MACA_BINS MACA_SOLK MACA_SOLB MACA_NCYC ] CloseSubFrame CreateLineTemplate MACSAD_TEMPLATE \ { 0.0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 } CreateLineTemplate MACSAD_PART_TEMPLATE \ { 0.0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8} CreateLine line \ message "SAD refinement macrocyles" \ widget TOG_MACSAD -toggleon label "SAD refinement" \ widget MACSAD_OPTION OpenSubFrame frame -toggle_display MACSAD_OPTION open CUSTOM hide OpenSubFrame frame -toggle_display EP_MODE open SAD CreateLine line \ label "OK" label "OB" label "OSS" label "AX" label "AO" label "AB" label "FDP" \ label "VA" label "VB" label "VP" label "VD" label "NCYC" \ format template MACSAD_TEMPLATE CreateExtendingFrame N_MACSAD phaser_EP_macs \ "Customize the SAD refinement" \ "Add another SAD macrocycle" \ [list TOG_MACSAD_K TOG_MACSAD_B TOG_MACSAD_XYZ TOG_MACSAD_OCC TOG_MACSAD_BFAC TOG_MACSAD_FDP \ TOG_MACSAD_SA TOG_MACSAD_SB TOG_MACSAD_SP TOG_MACSAD_SD MACSAD_NCYCL ] CloseSubFrame OpenSubFrame frame -toggle_display EP_MODE open MRSAD CreateLine line \ label "OK" label "OB" label "OSS" label "AX" label "AO" label "AB" label "FDP" \ label "VA" label "VB" label "VP" label "VD" label "PK" label "PB" label "NCYC" \ format template MACSAD_PART_TEMPLATE CreateExtendingFrame N_MACSAD phaser_EP_macs_part \ "Customize the SAD refinement" \ "Add another SAD macrocycle" \ [list TOG_MACSAD_K TOG_MACSAD_B TOG_MACSAD_XYZ TOG_MACSAD_OCC TOG_MACSAD_BFAC TOG_MACSAD_FDP \ TOG_MACSAD_SA TOG_MACSAD_SB TOG_MACSAD_SP TOG_MACSAD_SD TOG_MACSAD_PK TOG_MACSAD_PB MACSAD_NCYCL ] CloseSubFrame CloseSubFrame CreateLine line \ message "BINS: specify how the binning to all reflections will apply"\ widget TOG_BINS -toggleon \ label "Bins: Min" widget BINS_MIN label "Max" widget BINS_MAX label "Width" widget BINS_WIDTH \ message "Binning function: AS^3 + BS^2 + CS\ where S=1/reso."\ label "Cubic: A" widget BINS_A label "B" widget BINS_B label "C" widget BINS_C CreateLine line \ message "Restrain B-factors to Wilson B-factor" \ widget TOG_WILSON -toggleon label "B-factor Wilson Restraint" widget WILSON_ONOFF \ label "Sigma of restraint " \ widget WILSON_SIGMA \ toggle_display WILSON_ONOFF open ON CreateLine line \ message "Restrain B-factors to Wilson B-factor" \ widget TOG_WILSON -toggleon label "B-factor Wilson Restraint" widget WILSON_ONOFF \ toggle_display WILSON_ONOFF open OFF CreateLine line \ message "Restrain Anisotropic B-factors to be Isotropic" \ widget TOG_SPHERICITY -toggleon label "B-factor Sphericity Restraint" widget SPHERICITY_ONOFF \ label "Sigma of restraint " \ widget SPHERICITY_SIGMA \ toggle_display SPHERICITY_ONOFF open ON CreateLine line \ message "Restrain Anisotropic B-factors to be Isotropic" \ widget TOG_SPHERICITY -toggleon label "B-factor Sphericity Restraint" widget SPHERICITY_ONOFF \ toggle_display SPHERICITY_ONOFF open OFF CreateLine line \ widget TOG_CELL -toggleon \ label "Unit Cell: a" \ message "Cell dimensions (default from MTZ file) (CELL)" \ widget CELL_1 -width 8 \ label "b" \ widget CELL_2 -width 8 \ label "c" \ widget CELL_3 -width 8 \ label "alpha" \ widget CELL_4 -width 8 \ label "beta" \ widget CELL_5 -width 8 \ label "gamma" \ widget CELL_6 -width 8 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 -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 CreateLine line \ message "Single atom molecular replacement" \ widget EP_SAMR \ -command "phaser_EP_show_labin_F $arrayname" \ label "Only use merged F and SIGF for phasing (single atom MR)" 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 OpenSubFrame frame -toggle_display TNCS_USE open ON CreateLine line \ message "TNCS: translation vector in Angstroms" \ 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 "Angstroms" 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_PERCENT -toggleon \ label "Minimum percent of Patterson orgin peak " \ widget TNCS_PATT_PERCENT 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 CreateLine line \ message "TNCS: Paired atom restraints" \ label "TNCS: " \ widget TOG_TNCS_LINK -toggleon \ label "Use paired atom occupancy and B-factor restraint" \ widget TNCS_LINK_RESTRAINT \ label "Restraint sigma" \ widget TNCS_LINK_SIGMA \ toggle_display TNCS_LINK_RESTRAINT open ON CreateLine line \ message "TNCS: Paired atom restraints" \ label "TNCS: " \ widget TOG_TNCS_LINK -toggleon \ label "Use paired atom occupancy and B-factor restraint" \ widget TNCS_LINK_RESTRAINT \ toggle_display TNCS_LINK_RESTRAINT open OFF CreateLine line \ message "TNCS: Paired atom control" \ label "TNCS: " \ widget TOG_TNCS_PAIR_ONLY -toggleon \ label "Only add atoms in pairs" \ widget TNCS_PAIR_ONLY CloseSubFrame }