# ======================================================================= # phaser_ATOM.tcl -- # # Maximum Likelihood Molecular Replacement # # CCP4Interface # # ======================================================================= #------------------------------------------------------------------------------ proc phaser_ATOM_prereq { } { #------------------------------------------------------------------------------ if { ![file exists [FindExecutable phaser]] } { return 0 } return 1 } #------------------------------------------------------------------------ proc phaser_ATOM_setup { typedefVar arrayname } { #------------------------------------------------------------------------ upvar #0 $typedefVar typedef upvar #0 $arrayname array DefineMenu _spacegroup_option \ [list "mtz space group" "alternative spacegroup"] \ [list "SG_MTZ" "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" ] \ [ list "AVERAGE" "SOLVENT" "COMPONENT" ] DefineMenu _protnucleic \ [list "protein" "nucleic acid" ] [list "PROTEIN" "NUCLEIC" ] DefineMenu _rmsid_option \ [list "rms difference" "sequence identity" ] [list "RMS" "IDENT" ] set typedef(_mwseqnres_option) \ { menu { "molecular weight" "sequence file" "number of residues"} { "MW" "FASTA" "NRES"} } DefineMenu _search_method \ [list "full" "fast" ] [list "FULL" "FAST" ] DefineMenu _llgc_complete \ [list "on" "off" ] [list "ON" "OFF" ] 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(_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_ATOM_run { arrayname } { #------------------------------------------------------------------------ upvar #0 $arrayname array # The output file array is set up in phaser_ATOM.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 } } 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" } } } # #LLG completion checks if { ([GetValue $arrayname TOG_LLGC] == "1") } { if { ([GetValue $arrayname LLGC_COMPLETE] == "ON") } { 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 } } } } # Set up the array of input files: 1 or more mtz and maybe some pdb files set array(INPUT_FILES) "HKLIN_MAIN" # 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_ATOM_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_ATOM_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_ATOM_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_ATOM_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_ATOM_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_ATOM_tncs_use_and_valid {arrayname} { #------------------------------------------------------------------------ upvar #0 $arrayname array set array(TNCS_USE_AND_VALID) "1" if { [StringSame $array(TNCS_USE) OFF] } { set array(TNCS_USE_AND_VALID) "0" } } #------------------------------------------------------------------------ proc phaser_ATOM_set_reso {arrayname} { #------------------------------------------------------------------------ upvar #0 $arrayname array set array(RESOLUTION_DMIN_MR) [GetValue $arrayname RESOLUTION_DMIN] } #------------------------------------------------------------------------ proc phaser_ATOM_llgc { arrayname counter_f } { #------------------------------------------------------------------------ # Procedure to define a scattering for atom manually upvar #0 $arrayname array CreateLineTemplate BB { 0 0.32 0.57 } CreateLine line \ message "Atomtypes for LLG-maps" \ label "" label "or with atom type" \ widget LLGC_TYPE \ -command "phaser_ATOM_llgc_sad_toggle_update $arrayname " \ format template BB } # #------------------------------------------------------------------------ proc phaser_ATOM_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_ATOM_macm { arrayname counter_s } { #------------------------------------------------------------------------ global configure upvar #0 $arrayname array CreateLine line \ label " Rot" \ widget MACM_ROT \ label "Tran" \ widget MACM_TRA \ label "Bfac" \ widget MACM_BFAC \ label "Vrms"\ widget MACM_VRMS \ label "Last"\ widget MACM_LAST \ label "NCYC" \ widget MACM_NCYC -width 5 } #------------------------------------------------------------------------ proc phaser_ATOM_task_window {arrayname} { #------------------------------------------------------------------------ upvar #0 $arrayname array global configure if { [CreateTaskWindow $arrayname \ "Maximum Likelihood Single Atom Molecular Replacement"\ "Phaser" \ [ list "Define data" \ "Define search" \ "Define composition of the asymmetric unit" \ "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 \ 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 open CreateInputFileLine line \ "Enter MTZ file name (HKLIN)" \ "MTZ in " \ HKLIN_MAIN DIR_HKLIN_MAIN \ -setfileparam resolution_min RESOLUTION_DMAX \ -setfileparam resolution_max RESOLUTION_DMIN \ -setfileparam resolution_min RESOLUTION_AUTO_DMAX \ -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_ATOM_set_test_space_group $arrayname" \ -command "phaser_ATOM_set_reso $arrayname" CreateLabinLine line \ "Select amplitude (F) and sigma (SIGF)" \ HKLIN_MAIN "F" F {NULL} \ -sigma "SIGF" SIGF {NULL} CreateLine line \ message "Default is to take all data" \ widget TOG_RESOLUTION -toggleon \ label "Resolution range" \ message "Enter dmax, in Angstroms" \ widget RESOLUTION_DMAX label "A to" widget RESOLUTION_DMIN_MR label "A" 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 to run Phaser with" \ label "Run Phaser with" \ widget SPACEGROUP_OPTION OpenSubFrame frame -toggle_display SPACEGROUP_OPTION open SG_ALT CreateLine line \ label "Space Group:" widget PHASER_TEST_SG CloseSubFrame # $line.l2 configure -width 7 -background $configure(COLOUR_BACKGROUND) #======================================================================== # The "Define search" folder OpenFolder 2 open CreateLine line \ message "Atom type for which to search" \ label "Search single atom type" \ widget SEARCH_ATOM_TYPE -oblig \ label "Number of atoms " \ widget SEARCH_ATOM_NUM -oblig CreateLineTemplate AA { 0 0.23 0.32 0.57 } CreateLine line \ widget TOG_LLGC -toggleon \ label "LLG-map completion" \ widget LLGC_COMPLETE \ label "Complete with atom type " \ widget LLGC_FIRST_TYPE \ format template AA \ toggle_display LLGC_COMPLETE open ON hide CreateLineTemplate AB { 0 0.23 } CreateLine line \ widget TOG_LLGC -toggleon \ label "LLG-map completion" \ widget LLGC_COMPLETE \ format template AB \ toggle_display LLGC_COMPLETE open OFF hide OpenSubFrame frame -toggle_display LLGC_COMPLETE open ON hide CreateExtendingFrame N_LLGC phaser_ATOM_llgc \ "Add another atomtype" "Add another atomtype" \ [list LLGC_TYPE ] CloseSubFrame CreateLine line \ message "Default sigma cut-off = 6" \ widget TOG_LLGC_SIGMA -toggleon \ label "LLG-map sigma cut-off for adding new atom sites" \ widget LLGC_SIGMA CreateLine line \ message "Default clash distance is optical resolution" \ widget TOG_LLGC_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_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_NCYC -toggleon \ label "Maximum number of LLG-map completion cycles" \ widget LLGC_NCYC #======================================================================== # The "Define composition of the asymmetric unit" folder OpenFolder 3 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_ATOM_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 "Expert parameters" folder OpenFolder 4 closed 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 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 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 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 \ toggle_display PURGE_TRA_ONOFF open ON CreateLine line \ message "Choose whether to purge the solutions from TF and RNP \ (when searching multiple space groups)" \ widget TOG_PURGE_TRA -toggleon \ label "Purge translation peaks" \ widget PURGE_TRA_ONOFF \ toggle_display PURGE_TRA_ONOFF open OFF 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 multiple copies in ASU " \ widget SEARCH_METHOD \ message "Choose whether to permute the order of the search set.\ Default is OFF." \ label "Permute search set" \ widget PERMUTATIONS_ONOFF \ toggle_display SEARCH_METHOD open FULL 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 multiple copies in ASU " \ widget SEARCH_METHOD \ message "Reduce RF peak cutoff on 2nd pass" \ label "Deep" \ widget SEARCH_DEEP \ label "Down percent" \ message "Value for reducing cutoff" \ widget SEARCH_DOWN_PERC \ toggle_display SEARCH_METHOD open FAST hide OpenSubFrame frame -toggle_display SEARCH_METHOD open [list FAST] 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 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 CreateLine line \ message "Default is to take all data in mtz file" \ widget TOG_RESOLUTION_AUTO -toggleon \ label "Resolution range for high resolution refinement" \ message "Enter dmax, in Angstroms" \ widget RESOLUTION_AUTO_DMAX \ label "A to" \ widget RESOLUTION_AUTO_DMIN \ label "A" 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_ATOM_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 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" \ 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_ATOM_tncs_use_and_valid $arrayname" \ toggle_display TNCS_USE open OFF #======================================================================== # The "Output control" folder OpenFolder 5 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 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.\ Default depends on mode." \ 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_MAPS -toggleon \ label "Output log-likelihood gradient map coefficients" \ widget LLGC_MAPS #======================================================================== # The "Developer parameters" folder OpenFolder 6 closed CreateLine line \ label "Do not alter these parameters" -italic CreateLine line \ message "Select whether or not to rescore fast search solutions" \ widget TOG_RESCORE_TRA -toggleon \ label "Rescoring translation" \ widget RESCORE_ONOFF_TRA 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 "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_ATOM_maca \ "Customize the anisotropic refinement" \ "Add another anisotropic macrocycle" \ [list MACA_ANIS MACA_BINS MACA_SOLK MACA_SOLB MACA_NCYC ] CloseSubFrame 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_ATOM_macm \ "Customize the MR refinement" \ "Add another MR macrocycle" \ [list MACM_ROT MACM_TRA MACM_BFAC MACM_VRMS MACM_LAST MACM_NCYC ] 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 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 CreateLine line \ widget TOG_PACK_COMPACT -toggleon \ label "Pack molecules into compact group " \ widget PACK_COMPACT_ONOFF CreateLine line \ message "Select whether clustered or raw peaks are to be rescored" \ widget TOG_PEAKS_TRA_CLUSTER -toggleon \ label "Translation clustering" \ widget PEAKS_TRA_CLUSTER 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: Number of molecules/assemblies related by TNCS vector" \ label "TNCS: " \ widget TOG_TNCS_NMOL -toggleon \ label "Number of molecules/assemblies related by TNCS " \ widget TNCS_NMOL CreateLine line \ message "TNCS: refine rotation angles" \ label "TNCS: " \ widget TOG_TNCS_REFI_ROT -toggleon \ label "Refine TNCS rotations prior to translation function " \ widget TNCS_REFI_ROT 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