# ====================================================================== # loopy.tcl -- # # CCP4Interface # # ======================================================================= #---------------------------------------------------------------------- proc loopy_prereq {} { #---------------------------------------------------------------------- if { [GetEnvPath warpbin 0] == "" } { return 0 } else { return 1 } } #--------------------------------------------------------------------- proc loopy_setup { typedefVar arrayname } { #--------------------------------------------------------------------- upvar #0 $typedefVar typedef upvar $arrayname def_array global env # Confirm that the user has sourced the arpwarp setup script if { [info exists env(warpbin)] == 0 } { WarningMessage "Please check your shell startup file does source ARP/wARP 7.5. Then open another terminal window and re-launch CCP4i." return 0 } set warpbin [ GetEnvPath warpbin ] DefineMenu _loopy_fit_target [list "Weighted means" \ "Correlation" ] [list 0 1 ] DefineMenu _loopy_grid_type [list "Regular" "Random"] [list 0 1 ] DefineMenu _mode_loopy [list "Single loop" "All loops"] [list 0 1 ] set typedef(_loopfit_exe) { file LOOPFIT "loopfit" "executable for real-space refinement" {} {} } set typedef(_warpbin_dir) { default_dir {$warpbin} {warpbin} } set typedef(_nmol_int) { menu { "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" "16" "17" "18" "19" "20" } { 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 } } set typedef(_meth_is_seleno) { menu { "are" "are not" } { 1 0 } } set typedef(_loopy_nterm_menu) { varmenu N_ANCHOR_ID_MENU {} 8 } set typedef(_loopy_cterm_menu) { varmenu C_ANCHOR_ID_MENU {} 8 } #Below is needed, otherwise the widget N_ANCHOR and C_ANCHOR are # unsufficiently recognised... thus the -command option doesn't work # PLUS: update the menu's if the pdb was already filled in if {[ElementExists $arrayname PDB_INPUT_FILENAME]} { set tmp_input [GetValue $arrayname PDB_INPUT_FILENAME] if { [file exists $tmp_input] } { # loopy_update_anchor_menus $arrayname } else { UpdateVariableMenu $arrayname initialise 0 N_ANCHOR_ID_MENU {""} UpdateVariableMenu $arrayname initialise 0 C_ANCHOR_ID_MENU {""} set def_array(N_ANCHOR) "" set def_array(C_ANCHOR) "" } } else { UpdateVariableMenu $arrayname initialise 0 N_ANCHOR_ID_MENU {""} UpdateVariableMenu $arrayname initialise 0 C_ANCHOR_ID_MENU {""} set def_array(N_ANCHOR) "" set def_array(C_ANCHOR) "" } DefineMenu _map_input_mode [list "an existing map" \ "phases from MTZ file to calculate map"] \ [list MAP MTZ] #set array(CHAIN_ID_MENU) [ list "A" ] #DefineMenu _loopy_chain_id [GetValue array CHAIN_ID_MENU ] return 1 } #----------------------------------------------------------------------- proc loopy_task_window { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array if { ![CreateTaskWindow $arrayname \ "ARP/wARP Version 7.5.0: Loop Building" "ARP/wARP" \ [ list "Definition of the loop(s) (required parameters)" \ "Settings for generating loops" \ "Selecting best loops" "Selecting best CAs" \ "Generating CAs" "Density Handling" \ "Crystal Parameters (obtained from map/mtz file)" \ "Real-space refinement" \ "Log files of Loopy" ] \ ] } { return 0 } set help_source [file join [GetEnvPath warpdoc] loopy.html ] SetProgramHelpFile $help_source set array(NO_SEQUENCE) 1 #------------------------------------------------------------------------------ OpenFolder protocol CreateTitleLine line TITLE set arplogo [image create photo -file [ FileJoin [GetEnvPath warpbin] ARP_logo_small.gif ] ] set logo [label $line.log -image $arplogo] pack $logo CreateLine line \ message "Select input mode" \ label "For building loops use" \ help protocol \ widget MAP_INPUT_MODE CreateLine line \ message "Select mode for loop building: either one specific, or all" \ label "Mode for loop building" \ help protocol \ widget MODE_LOOPY \ -command "loopy_set_use_sequence $arrayname" #------------------------------------------------------------------------------ OpenFolder file # Density input (either MAP or MTZ) : OpenSubFrame frame -toggle_display MAP_INPUT_MODE open MAP CreateInputFileLine line \ "Best current electron density map" \ "Enter input map filename " \ MAP_FILENAME DIR_MAP_FILENAME \ -fileout EXT_MAP_FILENAME DIR_EXT_MAP_FILENAME "_ext" \ -help files \ -setfileparam space_group_name SPACEGROUP \ -setfileparam cell CELL \ -command "loopy_update_spacegroup $arrayname" CloseSubFrame # OR MTZ file ... (with optional FOM) OpenSubFrame frame -toggle_display MAP_INPUT_MODE open MTZ CreateInputFileLine line \ "Mtz file with phases for map calculation" \ "MTZ in" \ MTZ_FILENAME DIR_MTZ_FILENAME \ -help files \ -fileout MAP_FROM_MTZ DIR_MAP_FROM_MTZ "_loopy" \ -setfileparam space_group_number 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 CreateLabinLine line \ "Choose F for map calculation" MTZ_FILENAME \ "Fmap" F1 {FWT 2FOFCWT FP F} CreateLabinLine line \ "Choose Phi for map calculation" MTZ_FILENAME \ "PHImap" PHI {PHWT PH2FOFCWT PHIDM PHIDM } CloseSubFrame CreateInputFileLine line \ "Input PDB" \ "Protein model for loop building" \ PDB_INPUT_FILENAME DIR_PDB_INPUT_FILENAME \ -help files \ -fileout SAVE_LOOP_NAME DIR_SAVE_LOOP_NAME "_loop" \ -fileout SAVE_PROP_PDB DIR_SAVE_PROP_PDB "_proposed" \ -fileout OUTPUT_PDB DIR_OUTPUT_PDB "_loopy" \ -setfileparam space_group_name SPACEGROUP \ -setfileparam cell CELL \ -command "loopy_update_anchor_menus $arrayname ; loopy_update_spacegroup $arrayname ; loopy_update_basename $arrayname ; loopy_update_proposed_PDB $arrayname " OpenSubFrame frame -toggle_display MODE_LOOPY open 0 CreateLine line \ message "Indicate whether a pir-file is used to define the residues in the loop" \ label "Use pir-file to define the loop sequence" \ help files \ widget USE_PIR_FILE CloseSubFrame OpenSubFrame frame -toggle_display USE_PIR_FILE open 1 closed CreateExtendingFrame NSEQFILES pir_seq_in \ "Add an input sequence as a PIR file" \ "Add input PIR file" \ [list SEQIN DIR_SEQIN ] \ -dependentframe molau \ -edit set_nrestotal CloseSubFrame OpenSubFrame frame -toggle-display MODE_LOOPY open 0 closed CreateOutputFileLine file_line \ "Choose name format for the generated loop files" \ "New loops output file" \ SAVE_LOOP_NAME DIR_SAVE_LOOP_NAME \ -help files add_file_command $file_line "loopy_update_basename $arrayname" CreateOutputFileLine prop_file_line \ "Choose name format for the proposed full pdb files" \ "Protein and new loops combined output file" \ SAVE_PROP_PDB DIR_SAVE_PROP_PDB \ -help files add_file_command $prop_file_line "loopy_update_proposed_PDB $arrayname" CloseSubFrame OpenSubFrame frame -toggle-display MODE_LOOPY open 1 closed CreateOutputFileLine file_line \ "Choose the filename for the new pdb" \ "Output file" \ OUTPUT_PDB DIR_OUTPUT_PDB \ -help files CloseSubFrame #------------------------------------------------------------------------------ OpenFolder 1 #Definition of the loops #build all loops using pir-file OpenSubFrame frame -toggle_display USE_PIR_FILE open 1 closed CreateExtendingFrame NSEQFILES molau \ "Number of molecules and residues in the AU" \ " " \ [list NMOL \ NRES \ NRESMOL \ MET_IS_SEL ] -noaddline CloseSubFrame OpenSubFrame frame -toggle_display INCLUDE_ALL open 1 CreateLine line \ message "Assume that all chains in the PDB represent protein, and used for loop building" \ label "Use all the chains of the PDB" \ help loop_def \ widget INCLUDE_ALL \ -command "loopy_set_include_chains $arrayname ; loopy_update_anchor_menus $arrayname" CloseSubFrame OpenSubFrame frame -toggle_display INCLUDE_ALL open 0 CreateLine line \ message "Assume that all chains in the PDB represent protein, and used for loop building" \ label "Use all the chains of the PDB" \ help loop_def \ widget INCLUDE_ALL \ -command "loopy_set_include_chains $arrayname ; loopy_update_anchor_menus $arrayname" \ message "Give the set of chains to use" \ label "Use chains" \ help loop_def \ widget INCLUDE_CHAINS \ -command "loopy_check_include_chains $arrayname ; loopy_update_anchor_menus $arrayname" CloseSubFrame #build a single loop setting the loop sequence by hand OpenSubFrame frame -toggle_display MODE_LOOPY open 0 closed CreateLine line \ message "Select N-term anchor of the loop" \ label "Build a loop between residues" \ help loop_def \ widget C_ANCHOR -command "loopy_update_loop_definition $arrayname" \ label "and" \ help loop_def \ message "Select C-term (of protein) anchor of the loop" \ widget N_ANCHOR -command "loopy_update_loop_definition $arrayname" \ message "Give number of peptides INCLUDING anchors" \ label "; the length of the loop is" \ help loop_def \ widget LOOP_LENGTH -width 3 -command "loopy_update_loops_to_build $arrayname" CreateLine line \ message "Loop sequence INCLUDING anchors" \ label "The loop sequence including the anchors residues above is" \ help loop_def \ widget LOOP_SEQUENCE -oblig \ -command "loopy_check_sequence $arrayname" \ toggle_display USE_PIR_FILE open 0 CloseSubFrame #settings for general loop building #------------------------------------------------------------------------------ OpenFolder 2 #Defining details for generating loops OpenSubFrame fram -toggle_display MODE_LOOPY open 1 CreateLine line \ message "Maximum number of residues per loop to build" \ label "Build loops up to" \ help gen_loop \ widget MAX_LOOP_LENGTH \ label "residues long (including anchors)" CreateLine line \ message "Extend loops shorter than a given number of residues (including anchors)" \ label "Extend loops smaller than" \ help gen_loop \ widget EXTEND_GAP_SMALLER_THAN \ label "residues (including anchors)" CloseSubFrame OpenSubFrame frame -toggle_display USER_SETTING_MAX_NO_CAS open 1 CreateLine line \ message "Maximum number of CAs kept per node in the loop tree" \ help gen_loop \ widget USER_SETTING_MAX_NO_CAS \ label "Override default for maximum number of CAs kept per node in the loop tree" \ message "Maximum number of CAs kept per node in the loop tree" \ help gen_loop \ widget MAX_NO_CAS_KEPT -width 4 \ label "\tForce minimum number of CAs" \ help gen_loop \ widget FORCE_MIN_CAS_KEPT -width 4 CloseSubFrame OpenSubFrame frame -toggle_display USER_SETTING_MAX_NO_CAS open 0 CreateLine line \ message "Override the default, and variable (!) maximum number of CAs kept per node in the loop tree" \ help gen_loop \ widget USER_SETTING_MAX_NO_CAS \ label "Override the default maximum number of CAs per node" \ message "Set minimum number of CAs kept per node (overriding the threshold)" \ label "\tForce minimum number of CAs" \ help gen_loop \ widget FORCE_MIN_CAS_KEPT -width 4 CloseSubFrame CreateLine line \ message "Set number of best loops to save" \ label "Suggest " \ help files \ widget SAVE_BEST_NUMBER \ toggle_display MODE_LOOPY open 0 \ label "alternatives for each loop " #------------------------------------------------------------------------------ OpenFolder 3 closed #Selecting best loops CreateLine line \ label "Pruning aberrant loops" CreateLine line \ message "Maximum distance between the (symmetry mates) of the loop anchors" \ label "\tMaximum loop length (in A)" \ help loop_selection \ widget MAX_DISTANCE_BETWEEN_ANCHORS CreateLine line \ message "Deviation from CA-CA bond length of end loop and connecting fragment" \ label "\tDeviation distance loop connection" \ help loop_selection \ widget LOOP_RMS CreateLine line \ message "Number of loops during pruning based on density correlation of CAs" \ label "\tCA density correlation threshold" \ help loop_selection \ widget LOOP_DENSITY_CUTOFF_NO CreateLine line \ message "Threshold according to structural likelihood connection" \ label "\tStructural threshold" \ help loop_selection \ widget LOOP_STRUCTURE_THRESHOLD CreateLine line \ message "Override threshold to secure a minimum of loops at this stage" \ label "\t\tMinimum loop number for this stage " \ help loop_selection \ widget LOOP_STRUCTURE_MIN_NO CreateLine line \ message "Maximum number of loops kept based on structure" \ label "\t\tMaximum loop number for this stage" \ help loop_selection \ widget LOOP_STRUCTURE_CUTOFF_NO CreateLine line \ message "Loop selection based on the density fit of planes for main-chain atoms through succesive CA-pairs" \ label "\t\tLoops kept after building the main-chain atoms" \ help loop_selection \ widget MAX_LOOPS_AFTER_MC_PLANE CreateLine line \ message "Number of best loops kept, selected on the density fit of the main chain (after building the loops in both directions" \ label "\tMain chain density correlation threshold" \ help loop_selection \ widget LOOP_MAIN_CHAIN_DENS_NO #------------------------------------------------------------------------------ OpenFolder 4 closed #Selecting best CAs CreateLine line \ message "Likelihood threshold for rejecting generated CAs" \ label "Likelihood threshold" \ help CA_selection \ widget LIKELIHOOD_THRESHOLD -width 5 \ message "Show weights of different aspects contributing to threshold" \ label "\tShow details" \ widget SHOW_DETAILS_LIKELIHOOD OpenSubFrame frame -toggle_display SHOW_DETAILS_LIKELIHOOD open 1 CreateLine line \ message "Weight for the likelihood for CA-CA distance" \ label "\tWeight distance " \ help CA_selection \ widget WEIGHT_DISTANCE -width 4 CreateLine line \ message "Weight for the density correlation of the CA" \ label "\tWeight density " \ help CA_selection \ widget WEIGHT_DENSITY -width 4 CreateLine line \ message "Weight for the likelihood for the pentapeptide structure" \ label "\tWeight structure" \ help CA_selection \ widget WEIGHT_STRUCTURE -width 4 CreateInputFileLine line \ "Probability table for pentapeptide in C-terminus direction" \ "\tStructure table to C" \ STRUCTURE_TO_C DIR_STRUCTURE_TO_C \ -help CA_selection CreateInputFileLine line \ "Probability table for pentapeptide in N-terminus direction" \ "\tStructure table to N" \ STRUCTURE_TO_N DIR_STRUCTURE_TO_N \ -help CA_selection CloseSubFrame CreateLine line \ message "Set a measure for the minimum distance between generated CAs" \ label "Minimum distance CAs " \ help CA_selection \ widget MINIMAL_DISTANCE -width 4 #------------------------------------------------------------------------------ OpenFolder 5 closed #generating CAs OpenSubFrame frame -toggle_display GRID_TYPE open 0 CreateLine line \ message "Select way to generate a shell of CAs" \ label "Select generation CA shell" \ help CA_generation \ widget GRID_TYPE CreateLine line \ message "Number of CAs in a shell" \ label "\tNumber of CAs" \ help CA_generation \ widget GRID_NUMBER -width 5 CreateLine line \ message "Set the distance between successive CAs" \ label "\tCA-CA distance" \ help CA_generation \ widget CA_DISTANCE CloseSubFrame OpenSubFrame frame -toggle_display GRID_TYPE open 1 CreateLine line \ message "Select way to generate a shell of CAs" \ label "Select generation CA shell" \ help CA_generation \ widget GRID_TYPE CreateLine line \ message "Number of CAs in a shell" \ label "\tNumber of CAs" \ help CA_generation \ widget GRID_NUMBER -width 5 CreateLine line \ message "Set the distance between successive CAs" \ label "\tCA-CA distance" \ help CA_generation \ widget CA_DISTANCE CreateLine line \ message "Set the thickness of the shell" \ label "\tShell thickness" \ help CA_generation \ widget SHELL_THICKNESS -width 4 CreateLine line \ message "SD of the gaussian describing the distance probability" \ label "\tSD CA-CA distance" \ help CA_generation \ widget CA_DISTANCE_ERROR -width 4 CloseSubFrame CreateLine line \ message "Keep CAs with a negative density halfway between CA-CA" \ label "Keep CAs with negative density halfway" \ help CA_generation \ widget KEEP_NEG_DENS_HALFWAY #------------------------------------------------------------------------------ OpenFolder 6 closed #density handling OpenSubFrame frame -toggle_display SHOW_DETAILS_DENSITY open 0 CreateLine line \ message "Choose method to determine the density fit of the loops. Note: weighted means has a fast implementation" \ label "Scoring the density fit of the loops by" \ help density \ widget FITTARGET \ message "\tShow details density handling" \ label "Density details" \ widget SHOW_DETAILS_DENSITY CloseSubFrame OpenSubFrame frame -toggle_display SHOW_DETAILS_DENSITY open 1 CreateLine line \ message "Choose method to determine the density fit of the loops. Note: weighted means has a fast implementation" \ label "Scoring the density fit of the loops by" \ help density \ widget FITTARGET \ message "\tShow details density handling" \ label "Density details" \ widget SHOW_DETAILS_DENSITY CreateLine line \ label "Details on density handling:" CreateLine line \ message "Atom radius used to determine density correlation" \ label "\tAtom radius" \ help density \ widget ATOM_RADIUS CreateLine line \ message "B factor used for main chain atoms (so those in the PDB are ignored)" \ label "\tB factor (main chain atoms)" \ help density \ widget B_FACTOR CreateLine line \ message "B factor used for side chain atoms (so those in the PDB are ignored)" \ label "\tB factor (side chain atoms)" \ help density \ widget B_FACTOR_SIDE_CHAIN CreateLine line \ message "Remove atoms from the density by setting the density to -factor*density" \ label "\tRemove atoms by factor " \ help density \ widget REMOVAL_FACTOR CreateLine line \ message "After loop building, check the density correlation of main chain atoms of residues" \ label "\tDensity threshold residues " \ help density \ widget OVERLAP_REMOVAL_THRESHOLD CreateLine line \ message "After loop building, check the density correlation of dummy atoms" \ label "\tDensity threshold dummies" \ help density \ widget DUMMY_REMOVAL_THRESHOLD CloseSubFrame #------------------------------------------------------------------------------ OpenFolder 7 closed CreateLine line \ message "Space group (from map)" \ label "Space group" \ help crystal_params \ varlabel SPACEGROUP CreateLine line \ message "Cell dimensions (default taken from MTZ file" \ label "Cell a=" \ help crystal_params \ varlabel CELL_1 \ label " b=" \ varlabel CELL_2 \ label " c=" \ varlabel CELL_3 CreateLine line \ label " alpha=" \ help crystal_params \ varlabel CELL_4 \ label "beta=" \ varlabel CELL_5 \ label "gamma=" \ varlabel CELL_6 #------------------------------------------------------------------------------ OpenFolder 8 closed #Real-space refinement CreateLine line \ message "Choice whether to run real-space refinement on the loop regions in the output PDBs" \ label "Apply real-space refinement" \ help refinement \ widget REFINEMENT OpenSubFrame frame -toggle_display REFINEMENT open 1 CreateLine line \ message "Extend the region of the real-space refinement by a number of residues on BOTH sides of the loop" \ label "Extend the region for real-space refinement by " \ widget EXTEND_REFINEMENT \ label "residues" \ help refinement CreateInputFileLine line \ "Loopfit executable, used for the real-space refinemet of loop regions" \ "Loopfit executable" \ LOOPFIT_EXE_FILENAME DIR_LOOPFIT_EXE_FILENAME \ -toggle REFINEMENT \ -help refinement CreateOutputFileLine line \ "Filename for the loopfit log, used for the real-space refinement of loop regions" \ "Loopfit log" \ LOOPFIT_LOG_FILENAME DIR_LOOPFIT_LOG_FILENAME \ -toggle REFINEMENT \ -help refinement CloseSubFrame #------------------------------------------------------------------------------ OpenFolder 9 closed #log files CreateLine line \ message "Level at which to save messages from Loopy (0-9)" \ label "Message level " \ help logs \ widget MESSAGE_LEVEL CreateLine line \ message "Level at which to abort Loopy (0-9)" \ label "Abort level " \ help logs \ widget ABORT_LEVEL CreateOutputFileLine line \ "Filename for messages" \ "Message file " \ MESSAGE_FILENAME DIR_MESSAGE_FILENAME \ -help logs CreateOutputFileLine line \ "Filename for messages in XML format" \ "XML output file" \ XML_MESSAGE_FILENAME DIR_XML_MESSAGE_FILENAME \ -help logs } #--------------------------------------------------------------------- proc loopy_run { arrayname } { #--------------------------------------------------------------------- upvar #0 $arrayname array #Check input map/mtz set tmp_input_mode [GetValue $arrayname MAP_INPUT_MODE] if { [StringSame $tmp_input_mode "MAP"] } { set array(INPUT_FILES) " MAP_FILENAME " if { [loopy_get_value $arrayname "MAP_FILENAME" "filename of input map" "file" tmp_input_map ] } { if {![file exists $tmp_input_map] || [file isdirectory $tmp_input_map ]} { WarningMessage " In the file folder:\n In mode MAP, please insert \n a existing file for in the input map " return 0 } } else { return 0 } } else { if { [loopy_get_value $arrayname "MTZ_FILENAME" "filename of input mtz" "file" tmp_input_mtz] } { set array(INPUT_FILES) " MTZ_FILENAME " if {![file exists $tmp_input_mtz] || [file isdirectory $tmp_input_mtz ]} { WarningMessage " In the file folder:\n In mode MTZ, please insert \n a existing file for in the input mtz " return 0 } if {[loopy_get_value $arrayname "F1" "F" "file" tmp_f1]} { if { [StringSame $tmp_f1 "Unassigned" ]} { WarningMessage " In the file folder:\n Please enter a value for F\n It is needed to compute the map " return 0 } } else { return 0 } if {[loopy_get_value $arrayname "PHI" "PHI" "file" tmp_phi]} { if { [StringSame $tmp_phi "Unassigned" ] } { WarningMessage " In the file folder:\n Please enter a value for PHI\n It is needed to compute the map " return 0 } } else { return 0 } if {! [loopy_get_value $arrayname "MAP_FROM_MTZ" "output filename for calculated map" "file" tmp_output_map ]} { return 0 } } else { return 0 } } #check presence input pdb filename if {[loopy_get_value $arrayname "PDB_INPUT_FILENAME" "filename input PDB" "file" tmp_input_pdb ]} { append array(INPUT_FILES) " PDB_INPUT_FILENAME " if { ![file exists $tmp_input_pdb] || [file isdirectory $tmp_input_pdb ] } { WarningMessage " In the file folder:\n Please insert a proper filename for the input PDB " return 0 } } else { return 0 } #check presence input pir(s) if needed set tmp_mode_loopy [GetValue $arrayname MODE_LOOPY] set use_pir_file [GetValue $arrayname USE_PIR_FILE] if { $tmp_mode_loopy==1 } { if { $use_pir_file==0 } { WarningMessage " In the file folder:\n An error has occured. Please use pir files in the mode Build all Loops" return 0 } } if { $use_pir_file == 1 } { if {[loopy_get_value $arrayname "NSEQFILES" "number of sequence files" "file" tmp_seq_n ]} { for { set n 1 } { $n <= $tmp_seq_n } {incr n } { if { ![file exists [GetFullFileName1 $array(SEQIN,$n) $array(DIR_SEQIN,$n) ] ] } { WarningMessage " In the file folder:\n Can not open Sequence input file " return 0 } else { append array(INPUT_FILES) " SEQIN,$n " } if { $array(NMOL,$n) == "" } { WarningMessage " In the folder Definition of the loop(s) parameters:\n You have to set the number of molecules " return 0 } } } } if {![loopy_check_include_chains $arrayname]} { WarningMessage " In the folder Definition of the loop(s):\n The list of chains to process doesn't comply with \n the expected format (A|B|...). Or an unexpected chain was given" return 0 } #check crystal parameters set tmp_spacegroup [GetValue $arrayname SPACEGROUP ] if { ![ loopy_get_value $arrayname "SPACEGROUP" "spacegroup name" "Crystal Parameters" tmp_spacegroup ] } { return 0 } else { loopy_update_spacegroup $arrayname if { ![GetValue $arrayname SPACEGROUP_NUMBER ]} { WarningMessage " In the folder Crystal Parameters:\n Couldn't convert the spacegroup name to a spacegroup number.\n Please insert a proper spacegroup name" return 0 } } if {![loopy_get_value $arrayname "CELL_1" "cell length a" "Crystal Parameters" tmpC1] } { return 0 } if {![loopy_get_value $arrayname "CELL_2" "cell length b" "Crystal Parameters" tmpC2] } { return 0 } if {![loopy_get_value $arrayname "CELL_3" "cell length c" "Crystal Parameters" tmpC3] } { return 0 } if {![loopy_get_value $arrayname "CELL_4" "cell angle alpha" "Crystal Parameters" tmpC4] } { return 0 } if {![loopy_get_value $arrayname "CELL_5" "cell angle beta" "Crystal Parameters" tmpC5] } { return 0 } if {![loopy_get_value $arrayname "CELL_6" "cell angle gamma" "Crystal Parameters" tmpC6] } { return 0 } loopy_calc_cell_volume [list $tmpC1 $tmpC2 $tmpC3 $tmpC4 $tmpC5 $tmpC6 ] tmp_volume if { $tmp_volume<=0 } { WarningMessage " In the folder Crystal Parameters:\n The volume of the cell is <=0\n Please check the cell dimensions. \n" return 0 } if { $tmpC1<=0 || $tmpC2<=0 || $tmpC3<=0 || $tmpC4<0 || $tmpC4>180 || $tmpC5<0 || $tmpC5>180 || $tmpC6<0 || $tmpC6>180} { WarningMessage " In the folder Crystal Parameters:\n Please check the cell dimensions" return 0 } #check loop definition if { $tmp_mode_loopy == 0 } { if {![loopy_get_value $arrayname "N_ANCHOR" "n-terminal anchor residue" "Definition of the loop(s)" tmp_nanchor] } { return 0 } if {![loopy_get_value $arrayname "C_ANCHOR" "c-terminal anchor residue" "Definition of the loop(s)" tmp_canchor] } { return 0 } if {![loopy_get_value $arrayname "LOOP_LENGTH" "length of the loop" "Definition of the loop(s)" tmp_length] } { return 0 } set use_pir_file [GetValue $arrayname USE_PIR_FILE] if { !$use_pir_file } { if {![loopy_get_value $arrayname "LOOP_SEQUENCE" "sequence of the loop" "Definition of the loop(s)" tmp_sequence] } { return 0 } } if { $tmp_length <=0 } { WarningMessage " In the folder Definition of the loop(s):\n Please enter a loop length larger than zero. " return 0 } else { if { !$use_pir_file } { if { $tmp_length != [string length $tmp_sequence] } { WarningMessage " In the folder Definition of the loop(s):\n The loop length (${tmp_length}) and the length of the given sequence ([string length $tmp_sequence]) don't comply\n Please check loop length and the loop sequence " return 0 } } } } else { if {![loopy_get_value $arrayname "MAX_LOOP_LENGTH" "length of the loop" "Settings for generating loops" tmp_length] } { return 0 } if { $tmp_length>15 } { WarningMessage " In the folder Settings for generating loops :\n The maximum loop length (${tmp_length}) is set larger than 15. Be aware that computation of this loop length can take a lot of time and memory " \ -button Acknowledge } } #check parameters for selecting the best loops if {![loopy_get_value $arrayname "MAX_DISTANCE_BETWEEN_ANCHORS" "the maximum loop length (in A)" "Selecting best loops" tmp_distance] } { return 0 } else { if { $tmp_distance<=0 && $tmp_distance!=-1} { WarningMessage " In the folder Selecting best loops:\n The maximum loop length (in A) should be larger than zero (or, to turn it off: -1). " return 0 } } if {![loopy_get_value $arrayname "LOOP_RMS" "error in distance between loop CA and connecting CA" "Selecting best loops" tmp_distance] } { return 0 } else { if { $tmp_distance<=0 } { WarningMessage " In the folder Selecting best loops:\n The error in the distance between the suggested loop CA \n and the connecting CA should be larger than zero. " return 0 } } if {![loopy_get_value $arrayname "LOOP_STRUCTURE_THRESHOLD" "structural threshold" "Selecting best loops" tmp_struct_threshold] } { return 0 } else { if { $tmp_struct_threshold > 0 } { set tmp_option [ ChooseOptionDialog "Positive threshold?" icon \ " In the folder Selecting best loops:\n The structure threshold is for the log of a probability, which is always negative.\n Are you certain you want a positive threshold?" \ { NO YES } 1 -default ] if { [StringSame $tmp_option "NO" ] } { return 0; } } } if {![loopy_get_value $arrayname "LOOP_STRUCTURE_MIN_NO" "the minimum number of loops to keep after structure checking" "Selecting best loops" tmp_struct_min] } { return 0 } else { if { $tmp_struct_min < 0 } { WarningMessage " In the folder Selecting best loops:\n The minimum number of loops to keep after checking on structure \n has to be >=0." return 0 } } if {![loopy_get_value $arrayname "LOOP_STRUCTURE_CUTOFF_NO" "the maximum number of loops to keep after structure checking" "Selecting best loops" tmp_struct_cutoff ] } { return 0 } else { if { $tmp_struct_cutoff == 0 || $tmp_struct_cutoff<-1} { WarningMessage " In the folder Selecting best loops:\n The maximum number of loops to keep after checking on structure \n has to be >0 (or -1 to set no maximum)." return 0 } if { $tmp_struct_cutoff < $tmp_struct_min && $tmp_struct_cutoff!=-1 } { WarningMessage " In the folder Selecting best loops:\n The minimum number of loops to keep after checking on structure \n exceeds the maximum number to keep.\n Please check." return 0 } } #check input folder Selecting best CAs #only need to check presence of a value if {![loopy_get_value $arrayname "LIKELIHOOD_THRESHOLD" "the likelihood threshold" "Selecting best CAs" tmp ] } { return 0 } if {![loopy_get_value $arrayname "WEIGHT_DISTANCE" "the weight for the distance likelihood" "Selecting best CAs" tmp ] } { return 0 } if {![loopy_get_value $arrayname "WEIGHT_DENSITY" "the weight for the density likelihood" "Selecting best CAs" tmp ] } { return 0 } if {![loopy_get_value $arrayname "WEIGHT_STRUCTURE" "the weight for the structural likelihood" "Selecting best CAs" tmp ] } { return 0 } #checking folder Generating CAs loopy_get_value $arrayname "GRID_TYPE" "type of grid" "Generating CAs" tmp_grid_type if { $tmp_grid_type == 1 } { #random grid -> extra parameters if {[loopy_get_value $arrayname "SHELL_THICKNESS" "thickness of CA shell" "Generating CAs" tmp_thickness]} { if { $tmp_thickness < 0 } { WarningMessage " In the folder Generating CAs: \n Please enter a positive value for the shell thickness." return 0 } } else { return 0 } if {[loopy_get_value $arrayname "CA_DISTANCE_ERROR" "standard deviation in distribution distance CA-CA" "Generating CAs" tmp_distance_error]} { if { $tmp_distance_error < 0 } { WarningMessage " In the folder Generating CAs: \n Please enter a positive value for the standard deviation in the gaussian distribution for the CA-CA distance." return 0 } } else { return 0 } } if {[loopy_get_value $arrayname "GRID_NUMBER" "number of CAs per shell" "Generating CAs" tmp_number]} { set tmp_number [ loopy_get_fibonacci $tmp_grid_type $tmp_number ] if { $tmp_number <= 0 } { WarningMessage " In the folder Generating CAs: \n Please enter a value larger than zero for the number of CAs per shell." return 0 } } else { return 0 } if {[loopy_get_value $arrayname "CA_DISTANCE" "the distance between succesive CAs" "Generating CAs" tmp_number]} { if { $tmp_number <= 0 } { WarningMessage " In the folder Generating CAs: \n Please enter a value larger than zero for the distance between successive CAs." return 0 } else { set tmp_error [ expr { abs ( $tmp_number - 3.8 ) } ] if { $tmp_error > 1 } { set tmp_option [ ChooseOptionDialog "Expected CA-CA distance ~ 3.8 A" icon \ " In the folder Generating CAs:\n Expected a CA-CA distance of around 3.8 A. \n Are you certain of $tmp_number A ?" \ { NO YES } 1 -default ] if { [StringSame $tmp_option "NO" ] } { return 0; } } } } else { return 0 } #check whether file exists if {![loopy_get_value $arrayname "STRUCTURE_TO_C" "the filename for the structure table towards C terminus" "Selecting best CAs (detailed settings)" tmp_structurefile_toc ] } { return 0 } else { if {! [file readable $tmp_structurefile_toc ] } { WarningMessage " In the folder Selecting best CAs (detailed settings)\n Can't read the file containing the structure table \n towards the C terminus. Please select a proper file." return 0 } } if {![loopy_get_value $arrayname "STRUCTURE_TO_N" "the filename for the structure table towards N terminus" "Selecting best CAs (detailed settings)" tmp_structurefile_ton ] } { return 0 } else { if {! [file readable $tmp_structurefile_ton ] } { WarningMessage " In the folder Selecting best CAs (detailed settings)\n Can't read the file containing the structure table \n towards the N terminus. Please select a proper file." return 0 } } if {![loopy_get_value $arrayname "MINIMAL_DISTANCE" "the filename minimal distance between selected CAs" "Selecting best CAs" tmp ] } { return 0 } if { [ loopy_get_value $arrayname "MAX_NO_CAS_KEPT" "maximum number of CAs selected" "Settings for generating loops" tmp_max_no_cas ] } { if { $tmp_max_no_cas <=0 } { WarningMessage " In the folder Settings for generating loops\n Please enter a value larger than zero \n for the maximum number of CAs selected." return 0 } } else { return 0 } if { [ loopy_get_value $arrayname "FORCE_MIN_CAS_KEPT" "the minimum number of CAs to try to keep" "Settings for generating loops" tmp_min_no_cas ] } { if { $tmp_max_no_cas < $tmp_min_no_cas } { WarningMessage " In the folder Settings for generating loops\n The minimum number of CAs to keep exceeds \n the maximum number. Please check" return 0 } } else { return 0 } #check folder density handling if { [ loopy_get_value $arrayname "ATOM_RADIUS" "the atom radius" "Density Handling" tmp_atom_radius ] } { if { $tmp_atom_radius<=0 } { WarningMessage " In the folder Density Handling\n Please set a value larger than zero for the atom radius" return 0 } } else { return 0 } if { ![ loopy_get_value $arrayname "B_FACTOR" "the b-factor for main chain atoms" "Density Handling" tmp ] } { return 0 } if { ![ loopy_get_value $arrayname "B_FACTOR_SIDE_CHAIN" "the b-factor for side chain atoms" "Density Handling" tmp ] } { return 0 } if { [ loopy_get_value $arrayname "REMOVAL_FACTOR" "'remove atoms by factor'" "Density Handling" tmp ] } { if { $tmp < 0 } { WarningMessage " In the folder Density Handling\n A factor smaller than zero will enhance the density at the spot of the atom. Please give a positive value" return 0 } } else { return 0 } if { ![ loopy_get_value $arrayname "OVERLAP_REMOVAL_THRESHOLD" "the density threshold to assume overlap of residues with the loop" "Density Handling" tmp ] } { return 0 } if { ![ loopy_get_value $arrayname "DUMMY_REMOVAL_THRESHOLD" "the density threshold to assume overlap of a dummy with the loop" "Density Handling" tmp ] } { return 0 } #check the refinement folder if { [loopy_get_value $arrayname "REFINEMENT" "applying real-space refinement" "Real-space refinement" tmp_refine] } { if { $tmp_refine==1 } { if { [loopy_get_value $arrayname "LOOPFIT_EXE_FILENAME" "loopfit executable for applying real-space refinement" "Real-space refinement" tmp_exe] } { if { ![file executable $tmp_exe]} { WarningMessage " In the folder Real-space refinement\n Please select the loopfit executable to apply the real-space refinement" return 0 } } else { WarningMessage " In the folder Real-space refinement\n Please select the loopfit executable to apply the real-space refinement" return 0 } if { [loopy_get_value $arrayname "EXTEND_REFINEMENT" "loopfit executable for applying real-space refinement" "Real-space refinement" tmp] } { if { $tmp<0 } { WarningMessage " In the folder Real-space refinement\n Please choose a positive number of residues to extend the region for real-space refinement" } } } } #check folder log names if { [ loopy_get_value $arrayname "MESSAGE_LEVEL" "the level for messages" "Log files of Loopy" tmp_message_level ] } { if { $tmp_message_level<0 || $tmp_message_level>8} { WarningMessage " In the folder Log files for Loopy\n The level for messages should be a value in the region\[0,8\]" return 0 } } else { return 0 } if { [ loopy_get_value $arrayname "ABORT_LEVEL" "the level for terminating the program" "Log files of Loopy" tmp_abort_level ] } { if { $tmp_abort_level<0 || $tmp_abort_level>8} { WarningMessage " In the folder Log files for Loopy\n The level for termination of the program should be a value in the region\[0,8\]" return 0 } } else { return 0 } set tmp_message [GetFullFileName0 $arrayname MESSAGE_FILENAME] set tmp_xml_message [GetFullFileName0 $arrayname XML_MESSAGE_FILENAME] # if { ![ loopy_get_value $arrayname "MESSAGE_FILENAME" "the name of the message file" "Log files of Loopy" tmp_message ] } { # return 0 # } else { # if { ![ file writable $tmp_message ] } { # WarningMessage " In the folder Log files of Loopy \n Can't write to the given message file.\n Please choose another filename." # } # } # if { ![ loopy_get_value $arrayname "XML_MESSAGE_FILENAME" "the name of the XML message file" "Log files of Loopy" tmp_xml_message ] } { # return 0 # } else { # if { ![ file writable $tmp_xml_message ] } { # WarningMessage " In the folder Log files of Loopy \n Can't write to the given XML message file.\n Please choose another filename." # } # } #check presence name for output loops if { ![ loopy_get_value $arrayname "SAVE_LOOP_NAME" "the name of the output loops" "file" tmp_loop_name ] } { return 0 } else { loopy_update_basename $arrayname set tmp_base_dir [ GetValue $arrayname SAVE_LOOP_DIR ] set tmp_base_name [ GetValue $arrayname SAVE_LOOP_BASENAME ] if { [string is space $tmp_base_name ] } { WarningMessage " Couldn't extract a format for the loop output.\n Please enter a proper name for the first output file. " return 0; } if { [StringSame $tmp_base_dir "/" ] } { set tmp_option [ ChooseOptionDialog "Writing to root directory?" icon \ " You have chosen the root directory to save the loops.\n Are you certain?" \ { NO YES } 1 -default ] if { [StringSame $tmp_option "NO" ] } { return 0; } } } #check presence name for output loops if { ![ loopy_get_value $arrayname "SAVE_PROP_PDB" "the name of the proposed full PDBs" "file" tmp_loop_name ] } { return 0 } else { loopy_update_proposed_PDB $arrayname set tmp_base_dir [ GetValue $arrayname SAVE_LOOP_PROP_DIR ] set tmp_base_name [ GetValue $arrayname SAVE_LOOP_PROP_BASE ] if { [string is space $tmp_base_name ] } { WarningMessage " Couldn't extract a format for the proposed full PDBs.\n Please enter a proper name for the first file. " return 0; } if { [StringSame $tmp_base_dir "/" ] } { set tmp_option [ ChooseOptionDialog "Writing to root directory?" icon \ " You have chosen the root directory to save the loops.\n Are you certain?" \ { NO YES } 1 -default ] if { [StringSame $tmp_option "NO" ] } { return 0; } } } source [SearchPath TOP src execute.tcl] return 1 } #--------------------------------------------------------------------- proc loopy_get_value { arrayname key description folder value } { #--------------------------------------------------------------------- upvar #0 $arrayname array upvar $value tmp_value set tmp_exists 0 set tmp_value [ GetValue $arrayname $key ] if { [ ElementExists $arrayname $key ] && ![ string is space $tmp_value ] } { set tmp_exists 1 } else { WarningMessage " In the folder $folder:\n Please insert a value for $description." } return $tmp_exists } #switch the default to use the sequence with the mode of loop building #--------------------------------------------------------------------- proc loopy_set_use_sequence { arrayname } { #--------------------------------------------------------------------- upvar #0 $arrayname array set tmp_value [ GetValue $arrayname MODE_LOOPY ] #with each switch to MODE_LOOPY == 1, return the value to 1... previously USE_PIR_FILE was set to MODE_LOOPY with each switch if { $tmp_value==1 } { set array(USE_PIR_FILE) $tmp_value } return 1 } #--------------------------------------------------------------------- proc loopy_get_fibonacci { grid_type grid_no } { #--------------------------------------------------------------------- if { !$grid_type } { #regular grid set number [ loopy_compute_fibonacci $grid_no ] return $number } else { return $grid_no } } #--------------------------------------------------------------------- proc loopy_compute_fibonacci { number } { #--------------------------------------------------------------------- set tmpFibA 0 set tmpFibB 1 set tmpFibC [ expr { $tmpFibA + $tmpFibB } ] if { $number != 0 } { while { $tmpFibC <= $number } { set tmpFibA $tmpFibB set tmpFibB $tmpFibC set tmpFibC [ expr { $tmpFibA + $tmpFibB } ] } return $tmpFibB } return 0 } #--------------------------------------------------------------------- proc loopy_calc_cell_volume { cell volumeVar } { #--------------------------------------------------------------------- #copy paste from CCP4I_TOP/utils/map_utils.tcl... CalcCellVolume missed a closing bracket #d_sum Calculate the cell volume #d_arg cell Cell dimensions #d_arg volumeVar Returned cell volume upvar $volumeVar volume # cell - input list of cell parameters # volume - return cell volume set dtor 3.1415927/180.0 set a [lindex $cell 0] set b [lindex $cell 1] set c [lindex $cell 2] set al [expr [lindex $cell 3] * $dtor ] set be [expr [lindex $cell 4] * $dtor ] set g [expr [lindex $cell 5] * $dtor ] set volume [ expr { ( $a * $b * $c ) * ( sqrt ( 1 + 2 * cos($al) * cos($be) * cos($g) - pow (cos($al) ,2) - pow (cos($be) ,2)- pow (cos($g) ,2) ) ) } ] } #--------------------------------------------------------------------- proc loopy_update_basename { arrayname } { #--------------------------------------------------------------------- upvar #0 $arrayname array set tmp_name [GetValue $arrayname SAVE_LOOP_NAME] if { ![ StringSame $tmp_name "" ] } { set tmp_dir [GetValue $arrayname DIR_SAVE_LOOP_NAME] set tmp_pos_dot [string last "." $tmp_name] set tmp_cur_pos [expr {$tmp_pos_dot - 1 } ] while { [string match {[0-9]} [string index $tmp_name $tmp_cur_pos] ] && $tmp_cur_pos > 0 } { set tmp_cur_pos [expr {$tmp_cur_pos - 1 } ] } if { $tmp_cur_pos > 0 } { set tmp_basename [string range $tmp_name 0 $tmp_cur_pos ] if { [string is space $tmp_basename ] } { WarningMessage " There are only blank spaces before the extension.\n Please enter a proper name. " set array(SAVE_LOOP_BASENAME) "" set array(SAVE_LOOP_DIR) "" return } } else { #no extension found set tmp_basename $tmp_name if { [string is space $tmp_basename] } { WarningMessage " There are only blank spaces before the extension.\n Please enter a proper name. " set array(SAVE_LOOP_BASENAME) "" set array(SAVE_LOOP_DIR) "" return } } # WarningMessage "Saving loops as:\n\n ${tmp_basename}.pdb " set array(SAVE_LOOP_BASENAME) [ file tail $tmp_basename ] set array(SAVE_LOOP_DIR) [ file dirname $tmp_basename ] } else { set array(SAVE_LOOP_BASENAME) "" set array(SAVE_LOOP_DIR) "" } } #--------------------------------------------------------------------- proc loopy_update_proposed_PDB { arrayname } { #--------------------------------------------------------------------- upvar #0 $arrayname array set tmp_name [GetValue $arrayname SAVE_PROP_PDB] if { ![ StringSame $tmp_name "" ] } { set tmp_dir [GetValue $arrayname DIR_SAVE_PROP_PDB] set tmp_pos_dot [string last "." $tmp_name] set tmp_cur_pos [expr {$tmp_pos_dot - 1 } ] while { [string match {[0-9]} [string index $tmp_name $tmp_cur_pos] ] && $tmp_cur_pos > 0 } { set tmp_cur_pos [expr {$tmp_cur_pos - 1 } ] } if { $tmp_cur_pos > 0 } { set tmp_basename [string range $tmp_name 0 $tmp_cur_pos ] if { [string is space $tmp_basename ] } { WarningMessage " There are only blank spaces before the extension.\n Please enter a proper name. " set array(SAVE_LOOP_PROP_BASE) "" set array(SAVE_LOOP_PROP_DIR) "" return } } else { #no extension found set tmp_basename $tmp_name if { [string is space $tmp_basename] } { WarningMessage " There are only blank spaces before the extension.\n Please enter a proper name. " set array(SAVE_LOOP_PROP_BASE) "" set array(SAVE_LOOP_PROP_DIR) "" return } } # WarningMessage "Saving loops as:\n\n ${tmp_basename}.pdb " set array(SAVE_LOOP_PROP_BASE) [ file tail $tmp_basename ] set array(SAVE_LOOP_PROP_DIR) [ file dirname $tmp_basename ] } else { set array(SAVE_LOOP_PROP_BASE) "" set array(SAVE_LOOP_PROP_DIR) "" } } #---------------------------------------------------------------------- proc pir_seq_in { arrayname counter } { #---------------------------------------------------------------------- upvar #0 $arrayname array global configure CreateInputFileLine line \ "Enter input sequence file $counter name" \ "Sequence file" \ SEQIN DIR_SEQIN ## -command "is_pir_file $arrayname $counter" } # #---------------------------------------------------------------------- proc molau { arrayname counter } { #---------------------------------------------------------------------- CreateLine line \ label "For sequence #$counter there are" \ widget NMOL -oblig \ -command "set_nres $arrayname $counter" \ label " molecules in the AU (" \ varlabel NRESMOL \ label " residues per molecule, " \ varlabel NRES \ label " total in the AU )." CreateLine line \ label "The Methionine residues of this molecule " \ widget MET_IS_SEL \ label " Seleno-Methionines." } #-------------------------------------------------------------------- proc set_nrestotal { arrayname args } { upvar #0 $arrayname array set nrestotal 0 for { set n 1 } { $n <= $array(NSEQFILES) } {incr n } { if { $array(NRES,$n) != "" } { set nrestotal [expr $array(NRES,$n) + $nrestotal ] } } set array(NRESTOTAL) $nrestotal } #--------------------------------------------------------------------- proc loopy_check_sequence { arrayname } { #--------------------------------------------------------------------- upvar #0 $arrayname array set sequence [string trim [GetValue $arrayname LOOP_SEQUENCE ] ] set looplength [GetValue $arrayname LOOP_LENGTH ] set pos_pep {[+AVFPQMILDEKRSTYHCNQWG]} set array(NO_SEQUENCE) 1 if { [string length $sequence ] != $looplength } { WarningMessage "Expected a sequence consisting of $looplength characters" set array(LOOP_SEQUENCE) "" } else { set okay 1 set unexpected "\n (index : character)" for {set i 0} {$i<$looplength} {incr i} { set peptide [string index $sequence $i] if { [string match -nocase $pos_pep $peptide ] == 0 } { set unexpected "$unexpected\n $i : $peptide" set okay 0 } } if { $okay == 0 } { set array(NO_SEQUENCE) 1 WarningMessage "Sequence contains unexpected characters:$unexpected\nPlease rectify the sequence" } else { set array(NO_SEQUENCE) 0 set array(LOOP_SEQUENCE) [string toupper [string trim [GetValue $arrayname LOOP_SEQUENCE ] ] ] } } } #------------------------------------------------------------------------ proc loopy_update_spacegroup { arrayname } { #------------------------------------------------------------------------ upvar #0 $arrayname array set array(SPACEGROUP_NUMBER) [GetSpaceGroupNumber [GetValue $arrayname SPACEGROUP]] } #--------------------------------------------------------------------- proc loopy_update_loop_definition { arrayname } { #--------------------------------------------------------------------- upvar #0 $arrayname array set n_anchor [GetValue $arrayname N_ANCHOR] set n_anchor [string trim $n_anchor] set c_anchor [GetValue $arrayname C_ANCHOR] set c_anchor [string trim $c_anchor] set loop_length [GetValue $arrayname LOOP_LENGTH] if {![StringSame $n_anchor ""] && ![StringSame $c_anchor ""]} { set n_sep [string first " " $n_anchor] set n_chain [string trim [string range $n_anchor 0 $n_sep]] set n_res [string trim [string range $n_anchor $n_sep [string length $n_anchor] ] ] set c_sep [string first " " $c_anchor] set c_chain [string trim [string range $c_anchor 0 $c_sep]] set c_res [string trim [string range $c_anchor $c_sep [string length $c_anchor] ] ] if {[StringSame $n_chain $c_chain] && $c_res<$n_res} { set loop_length [expr {$n_res - $c_res + 1}] set array(LOOP_LENGTH) $loop_length } if { $loop_length > 15 } { WarningMessage "The selected loop is more than 15 residues long (including anchors). Please be aware that building this loop might use a lot of memory and take a lot of time" } #update loops_to_build set loops_to_build "${c_chain}${c_res}(${loop_length})${n_chain}${n_res}" set array(LOOPS_TO_BUILD) $loops_to_build } } #--------------------------------------------------------------------- proc loopy_update_loops_to_build { arrayname } { #--------------------------------------------------------------------- upvar #0 $arrayname array set n_anchor [GetValue $arrayname N_ANCHOR] set n_anchor [string trim $n_anchor] set c_anchor [GetValue $arrayname C_ANCHOR] set c_anchor [string trim $c_anchor] set loop_length [GetValue $arrayname LOOP_LENGTH] if {![StringSame $n_anchor ""] && ![StringSame $c_anchor ""]} { set n_sep [string first " " $n_anchor] set n_chain [string trim [string range $n_anchor 0 $n_sep]] set n_res [string trim [string range $n_anchor $n_sep [string length $n_anchor] ] ] set c_sep [string first " " $c_anchor] set c_chain [string trim [string range $c_anchor 0 $c_sep]] set c_res [string trim [string range $c_anchor $c_sep [string length $c_anchor] ] ] #update loops_to_build set loops_to_build "${c_chain}${c_res}(${loop_length})${n_chain}${n_res}" set array(LOOPS_TO_BUILD) $loops_to_build } } #------------------------------------------------------------------------ proc loopy_set_include_chains { arrayname } { #------------------------------------------------------------------------ # Set the variable INCLUDE_CHAINS according to the given pdb upvar #0 $arrayname array set tmp_all_chains [GetValue $arrayname INCLUDE_ALL] set tmp_include_chains "" if { $tmp_all_chains == 0 } { if { [llength [info procs PdbGetSegID]] <= 0 } { source [SearchPath TOP utils pdb_utils.tcl] } if { ![file exists [GetFullFileName0 $arrayname PDB_INPUT_FILENAME]] || ![PdbGetSegID [GetFullFileName0 $arrayname PDB_INPUT_FILENAME] chains chainranges] } { return 0 } set tmp_size [expr {[llength $chains] -1 } ] if {$tmp_size>-1} { set tmp_include_chains "(" for { set i 0 } { $i < $tmp_size } { incr i } { set tmp_include_chains "${tmp_include_chains}[lindex $chains $i]|" } set tmp_include_chains "${tmp_include_chains}[lindex $chains $tmp_size])" } } set array(INCLUDE_CHAINS) $tmp_include_chains } #------------------------------------------------------------------------ proc loopy_check_include_chains { arrayname } { #------------------------------------------------------------------------ # Check whether the variable INCLUDE_CHAINS complies with the format upvar #0 $arrayname def_array set tmp_include_chains [GetValue $arrayname INCLUDE_CHAINS] set tmp_new "" if { $tmp_include_chains == $tmp_new } { return 1 } #convert given string to list set tmp_length [string length $tmp_include_chains] #search start set tmp_start 0 set tmp_count 0 if { [llength [info procs PdbGetSegID]] <= 0 } { source [SearchPath TOP utils pdb_utils.tcl] } if { ![file exists [GetFullFileName0 $arrayname PDB_INPUT_FILENAME]] || ![PdbGetSegID [GetFullFileName0 $arrayname PDB_INPUT_FILENAME] chains chainranges] } { return 0 } while { $tmp_start==0 && $tmp_count<$tmp_length } { if { [string index $tmp_include_chains $tmp_count]=="\("} { set tmp_start 1 set tmp_new "\(" set tmp_count [expr {$tmp_count + 1} ] } elseif { [string index $tmp_include_chains $tmp_count]==" "} { set tmp_count [expr {$tmp_count + 1} ] } else { set tmp_count $tmp_length } } if { $tmp_start==0 } { WarningMessage "Please set the included chains, using the format (A|B|C|...)" return 0 } else { set tmp_chain 0 set tmp_sep 1 set tmp_current "" while { $tmp_count<$tmp_length && [string index $tmp_include_chains $tmp_count]!="\)" } { if { $tmp_chain } { if { [string index $tmp_include_chains $tmp_count ]=="|" } { set tmp_chain 0 set tmp_sep 1 } else { if { [ string index $tmp_include_chains $tmp_count]!=" "} { set tmp_current "${tmp_current}[string index $tmp_include_chains $tmp_count]" } } } else { if {$tmp_sep} { if {[lsearch $chains $tmp_current]!=-1} { set tmp_chain 1 set tmp_sep 0 set tmp_new "${tmp_new}$tmp_current|" set tmp_current "" } else { set tmp_chain 0 set tmp_sep 0 set tmp_current "" } if {[string index $tmp_include_chains $tmp_count]!=" " && $tmp_sep==0} { set tmp_chain 1 set tmp_current "${tmp_current}[string index $tmp_include_chains $tmp_count]" } } } set tmp_count [expr {${tmp_count}+1}] } if { [string index $tmp_include_chains $tmp_count]=="\)" } { if { $tmp_current == "" } { set tmp_new "${tmp_new}\)" } else { if {[lsearch $chains $tmp_current]!=-1} { set tmp_new "${tmp_new}${tmp_current}\)" } else { set tmp_new "${tmp_new}\)" } } return 1 } else { WarningMessage "Please set the included chains, using the format (A|B|C|...)" return 0 } } } #------------------------------------------------------------------------ proc loopy_get_include_chains { arrayname chain_list} { #------------------------------------------------------------------------ # Get the list of chains to use (needed for the drop down menus for the C/N Termini). # upvar #0 $arrayname def_array upvar $chain_list include_chains set tmp_include_chains [GetValue $arrayname INCLUDE_CHAINS] set tmp_new "" set include_chains [list] if { $tmp_include_chains == $tmp_new } { return 1 } set tmp_all [GetValue $arrayname INCLUDE_ALL] if { $tmp_all } { return 1 } #convert given string to list set tmp_length [string length $tmp_include_chains] #search start set tmp_start 0 set tmp_count 0 if { [llength [info procs PdbGetSegID]] <= 0 } { source [SearchPath TOP utils pdb_utils.tcl] } if { ![file exists [GetFullFileName0 $arrayname PDB_INPUT_FILENAME]] || ![PdbGetSegID [GetFullFileName0 $arrayname PDB_INPUT_FILENAME] chains chainranges] } { return 0 } while { $tmp_start==0 && $tmp_count<$tmp_length } { if { [string index $tmp_include_chains $tmp_count]=="\("} { set tmp_start 1 set tmp_count [expr {$tmp_count + 1} ] } elseif { [string index $tmp_include_chains $tmp_count]==" "} { set tmp_count [expr {$tmp_count + 1} ] } else { set tmp_count $tmp_length } } if { $tmp_start==0 } { return 1 } else { set tmp_chain 0 set tmp_sep 1 set tmp_current "" while { $tmp_count<$tmp_length && [string index $tmp_include_chains $tmp_count]!="\)" } { if { $tmp_chain } { if { [string index $tmp_include_chains $tmp_count ]=="|" } { set tmp_chain 0 set tmp_sep 1 } else { if { [ string index $tmp_include_chains $tmp_count]!=" "} { set tmp_current "${tmp_current}[string index $tmp_include_chains $tmp_count]" } } } else { if {$tmp_sep} { if {[lsearch $chains $tmp_current]!=-1} { set tmp_chain 1 set tmp_sep 0 lappend include_chains $tmp_current set tmp_current "" } else { set tmp_chain 0 set tmp_sep 0 set tmp_current "" } if {[string index $tmp_include_chains $tmp_count]!=" " && $tmp_sep==0} { set tmp_chain 1 set tmp_current "${tmp_current}[string index $tmp_include_chains $tmp_count]" } } } set tmp_count [expr {${tmp_count}+1}] } if { [string index $tmp_include_chains $tmp_count]=="\)" } { if { $tmp_current != "" } { if {[lsearch $chains $tmp_current]!=-1} { lappend include_chains $tmp_current } } } return 1 } } #------------------------------------------------------------------------ proc loopy_update_anchor_menus { arrayname } { #------------------------------------------------------------------------ # Update the chain variable menu (CHAIN_ID_MENU) which is used in # defining non-xtal symmetry restraints upvar #0 $arrayname def_array if { ![file exists [GetFullFileName0 $arrayname PDB_INPUT_FILENAME]] || ![PdbGetNandCTermini [GetFullFileName0 $arrayname PDB_INPUT_FILENAME] nTerms cTerms $arrayname] } { return 0 } UpdateVariableMenu $arrayname initialise 0 N_ANCHOR_ID_MENU $nTerms UpdateVariableMenu $arrayname initialise 0 C_ANCHOR_ID_MENU $cTerms set def_array(N_ANCHOR) "" set def_array(C_ANCHOR) "" set def_array(LOOP_LENGTH) 0 set def_array(LOOP_SEQUENCE) "" return 1 } #---------------------------------------------------------------------------- proc GetNoSpaceSegID { chainID segID } { #---------------------------------------------------------------------------- #chainID chainID of the residue in the PDB #segID segment ID of the residue in the PDB #return the segment ID to use. If segID is empty, use the chainID. replace (right justified) spaces with the letter A set cur_segID [string trim $segID] if { $cur_segID == "" } { set cur_setID $chainID } set cur_segID [string toupper $cur_segID] set cur_segID [string map { {} A} $cur_segID] set cur_length [expr 4 - [string length $cur_segID]] set cur_append [string repeat A $cur_length] append cur_append $cur_segID return $cur_append } #---------------------------------------------------------------------------- proc PdbGetNandCTermini { file nTermini cTermini arrayname} { #---------------------------------------------------------------------------- #d_sum Get a list of the chains and the first & last residue ids in a PDB file #d_desk Note: in this case first and last equate to lowest and highest numbering #d_arg file Input PDB file #d_arg chainVar Returned list of chain ids #d_arg chain_rangeVar Returned nested list of first and last residues in chains upvar $nTermini nTerm upvar $cTermini cTerm upvar #0 $arrayname def_array set chain {} set current_chain "" set current_id "" set residues {} set current_residue "" set nTerm {} set cTerm {} set chainMatchSegID 1 set chain_used [GetValue $arrayname INCLUDE_CHAINS] set use_all_chains [GetValue $arrayname INCLUDE_ALL] set chain_list [list] if { $use_all_chains==0 } { loopy_get_include_chains $arrayname chain_list } if { ![ReadFile $file text -split] } { WarningMessage "ERROR reading file $file" return 0 } foreach line $text { if { [regexp {^ATOM|^HETATM} $line] } { set current_chain [string range $line 21 21] set test_id [GetNoSpaceSegID $current_chain ""] set current_segid [string range $line 72 75] set current_segid [GetNoSpaceSegID $current_chain $current_segid] if { ![StringSame $current_chain " "] && ![StringSame $test_id $current_segid] } { set chainMatchSegID 0 } #always use the chain id (except when its absent) for version 7.1. Output an error when the seg id's would differ from the chain ids according to loopy set old_id $current_id set current_id $current_chain if { $current_chain eq " " } { set current_id [string range $current_segid 3 3] } if { [lsearch -exact $chain $current_id] == -1 } { # new chain set test_res [string trim [string range $line 22 25]] set restype [string trim [string range $line 17 19]] if { ![regexp HOH|WAT|H2O|SOL|DUM|DU0|DU1 $restype] } { if { $use_all_chains==1 || [ lsearch -exact $chain_list $current_chain ]!=-1 } { if { [llength $residues] > 0} { lappend cTerm [list $old_id $current_residue] } set residues [list $test_res] set current_residue $test_res lappend nTerm [list $current_id $current_residue] lappend chain $current_id } else { set residues {} } } } else { #old chain set test_res [string trim [string range $line 22 25]] set restype [string trim [string range $line 17 19]] if { ![regexp HOH|WAT|H2O|SOL|DUM|DU0|DU1 $restype] } { if { $use_all_chains==1 || [ lsearch -exact $chain_list $current_chain ]!=-1 } { if { [lsearch -exact $residues $test_res] < 0 } { lappend residues $test_res set diff [expr { $test_res - $current_residue} ] if { $diff != 1 } { lappend cTerm [list $current_id $current_residue] lappend nTerm [list $current_id $test_res] } set current_residue $test_res } } } } } } if { $chainMatchSegID == 0 } { WarningMessage "Please ensure that the pdb only contains either chain ID's or seg ID's.\n In most other cases, loopy will probably fail to run." return 0 } # puts "chain $chain chain_range $chain_range" return 1 } #---------------------------------------------------------------------------- proc PdbGetSegID { file chainVar chain_rangeVar args } { #---------------------------------------------------------------------------- #d_sum Get a list of the chains and the first & last residue ids in a PDB file #d_desk Note: in this case first and last equate to lowest and highest numbering #d_arg file Input PDB file #d_arg chainVar Returned list of chain ids #d_arg chain_rangeVar Returned nested list of first and last residues in chains #d_opt0 -nowat #d_opt1 Ignore atoms of type HOH|WAT|H2O|SOL #d_opt0 -atomid #d_opt1 Return the ids of the first and last atoms in a chain upvar $chainVar chain upvar $chain_rangeVar chain_range set chain {} set chain_range {} set last_res "" set first_res "" set water 1 set atomid 0 set nargs [llength $args]; set n 0 while { $n < $nargs } { switch -regexp -- [lindex $args $n] \ nowat { set water 0 # return the atom id (ie the atomid) rather than the residue id } atomid { set atomid 1 } incr n } if { ![ReadFile $file text -split] } { puts "ERROR reading file $file" return 0 } set chainMatchSegID 1 foreach line $text { if { [regexp {^ATOM|^HETATM} $line] } { set current_chain [string range $line 21 21] set test_id [GetNoSpaceSegID $current_chain ""] set current_segid [string range $line 72 75] set current_segid [GetNoSpaceSegID $current_chain $current_segid] if { ![StringSame $current_chain " "] && ![StringSame $test_id $current_segid] } { set chainMatchSegID 0 } # set current_chain [string range $line 21 21] # set current_segid [string range $line 72 75] # set current_segid [GetNoSpaceSegID $current_chain $current_segid] #always use the chain id (except when its absent) for version 7.1. Output an error when the seg id's would differ from the chain ids according to loopy set current_id $current_chain if { $current_chain eq " " } { set current_id [string range $current_segid 3 3] } if { [lsearch -exact $chain $current_id] < 0 } { lappend chain $current_id if { $last_res != "" } { lappend chain_range [list $first_res [string trim $last_res]] } if { $atomid } { set first_res [string trim [string range $line 6 10]] } else { set test_res [string trim [string range $line 22 25]] set first_res $test_res set last_res $test_res } lappend restype [string trim [string range $line 17 19]] } else { if { $atomid } { set last_res [string range $line 6 10] } else { set test_res [string trim [string range $line 22 25]] if { $test_res < $first_res } { set first_res $test_res } if { $test_res > $last_res } { set last_res $test_res } } } }} lappend chain_range [list $first_res [string trim $last_res]] if { !$water } { for {set n [expr [llength $restype] -1] } { $n >= 0 } { incr n -1 } { if { [regexp HOH|WAT|H2O|SOL [lindex $restype $n] ] } { set chain_range [lreplace $chain_range $n $n] set chain [lreplace $chain $n $n] } } } if { $chainMatchSegID == 0 } { WarningMessage "Please ensure that the pdb only contains either chain ID's or seg ID's.\n In most other cases, loopy will probably fail to run." return 0 } # puts "chain $chain chain_range $chain_range" return 1 }