# ====================================================================== # buccaneer.tcl -- # # CCP4Interface # # ======================================================================= #------------------------------------------------------------------------------ proc buccaneer_prereq { } { #------------------------------------------------------------------------------ if { ![file exists [FindExecutable cbuccaneer]] } { return 0 } return 1 } #------------------------------------------------------------------------ proc buccaneer_setup { typedefname arrayname } { #------------------------------------------------------------------------ upvar #0 $typedefname typedef set typedef(_seq_reliability) { menu { "definite" "probable" "possible" } { 0.99 0.95 0.80 } } set typedef(_ramachan_filter) { menu { "all" "helix" "strand" "nonhelix" } } set typedef(_ref_structureid) { menu { "1tqw" "1ajr" } } return 1 } #------------------------------------------------------------------------------ proc buccaneer_run { arrayname } { #------------------------------------------------------------------------------ upvar #0 $arrayname array global env if { $array(USEPHIW) == 0 && ( $array(HLAwrk) == "Unassigned" || \ $array(HLBwrk) == "Unassigned" || \ $array(HLCwrk) == "Unassigned" || \ $array(HLDwrk) == "Unassigned" ) } { WarningMessage "One or more input labels are unassigned. Please check that input labels are correctly set before rerunning the task" return 0 } if { $array(USEPHIW) == 1 && ( $array(PHIwrk) == "Unassigned" || \ $array(FOMwrk) == "Unassigned" ) } { WarningMessage "One or more input labels are unassigned. Please check that input labels are correctly set before rerunning the task" return 0 } if { $array(USEFREE) == 1 && ( $array(FREEwrk) == "Unassigned" ) } { WarningMessage "One or more input labels are unassigned. Please check that input labels are correctly set before rerunning the task" return 0 } if { $array(REFUSER) == 0 } { set base [FileJoin [GetEnvPath CLIBD] reference_structures] set code "$array(REFCODE)" set array(HKLINref) [FileJoin "$base" "reference-$code.mtz"] set array(XYZINref) [FileJoin "$base" "reference-$code.pdb"] set array(FPref) "FP.F_sigF.F" set array(SIGFPref) "FP.F_sigF.sigF" set array(HLAref) "FC.ABCD.A" set array(HLBref) "FC.ABCD.B" set array(HLCref) "FC.ABCD.C" set array(HLDref) "FC.ABCD.D" } set files "HKLINwrk" if { $array(DOSEQNC) == 1 } { set files "$files SEQINwrk" } if { $array(USEXYZIN) == 1 } { set files "$files XYZINwrk" } set array(INPUT_FILES) "$files" return 1 } #--------------------------------------------------------------------- proc buccaneer_task_window { arrayname } { #--------------------------------------------------------------------- upvar #0 $arrayname array if { [ CreateTaskWindow $arrayname \ "Chain tracing using Buccaneer" "Buccaneer" \ [ list \ "Options" \ "Build steps" \ "Optional parameters" \ ] ] == 0 } return # Set the name of the CCP4 program help file to use SetProgramHelpFile "cbuccaneer" #=PROTOCOL============================================================== OpenFolder protocol CreateTitleLine line TITLE #=FILES================================================================ OpenFolder file CreateLine line \ label "Data for (unsolved) work structure:" -italic \ label " (Note: perform phase improvement/density modification first)" CreateLine line \ message "Add new chains, residues or sequence to an exisiting model" \ widget USEXYZIN -width 4 \ label "Specify an initial model to be extended. " \ message "A heavy atom or MR model can help with sequencing" \ widget USEXYZSQ -width 4 \ label "Specify a heavy atom or MR model." OpenSubFrame pdbinwrk \ -toggle_display USEXYZIN open 1 CreateInputFileLine line \ "Enter input coordinate file name for (unsolved) work structure" \ "Work PDB in" \ XYZINwrk DIR_XYZINwrk CloseSubFrame OpenSubFrame seqinwrk \ -toggle_display DOSEQNC open 1 CreateInputFileLine line \ "Enter input sequence file name for (unsolved) work structure" \ "Work SEQ in" \ SEQINwrk DIR_SEQINwrk CloseSubFrame CreateInputFileLine line \ "Enter input reflection file name for (unsolved) work structure" \ "Work MTZ in" \ HKLINwrk DIR_HKLINwrk \ -fileout XYZOUT DIR_XYZOUT "_buccaneer" CreateLabinLine line \ "Observed amplitude (FP) and obligatory sigma (SIGFP)" \ HKLINwrk "FP" FPwrk [list FP FP.F_sigF.F ] \ -sigma "SIGFP" SIGFPwrk [list SIGFP FP.F_sigF.sigF] CreateLabinLine4 line \ "Choose Hendrickson-Lattman coefficients from phase improvement (i.e. DENSITY MODIFIED PHASES)" \ HKLINwrk "HLA" HLAwrk [list parrot.ABCD.A pirate.ABCD.A HLADM] \ -dependent "HLB" HLBwrk [list parrot.ABCD.B pirate.ABCD.B HLBDM] \ -dependent "HLC" HLCwrk [list parrot.ABCD.C pirate.ABCD.C HLCDM] \ -dependent "HLD" HLDwrk [list parrot.ABCD.D pirate.ABCD.D HLDDM] \ -toggle_display USEPHIW open 0 CreateLabinLine line \ "Choose phi/fom" \ HKLINwrk "PHI" PHIwrk [list PHIDM PHWT] \ -sigma "FOM" FOMwrk [list FOMDM FOM ] \ -toggle_display USEPHIW open 1 CreateLabinLine line \ "Choose F/phi" \ HKLINwrk "F" FMAPwrk [list parrot.F_phi.F pirate.F_phi.F FWT ] \ -sigma "PHI" PMAPwrk [list parrot.F_phi.phi pirate.F_phi.phi PHWT] \ -toggle_display USEFMAP open 1 CreateLabinLine line \ "Choose Free-R flag" \ HKLINwrk "Free R flag" FREEwrk [list FreeR_flag] \ -toggle_display USEFREE open 1 CreateLine line \ message "Optionally specify Free-R set" \ help colin-wrk-free \ label " Use Free-R flag:" \ widget USEFREE \ message "Optionally specify starting map coefficients" \ help colin-wrk-fc \ label " Use map coefficients:" \ widget USEFMAP \ message "Select this option if you don't have HL coefficients - e.g. after MR or SHELX" \ help colin-wrk-phifom \ label " Use PHI/FOM instead of HL coefficients:" \ widget USEPHIW OpenSubFrame pdbinseq \ -toggle_display USEXYZSQ open 1 CreateInputFileLine line \ "Enter input coordinate file name for heavy atom/MR structure to help with sequencing" \ "HA/MR PDB in" \ XYZINseq DIR_XYZINseq CloseSubFrame CreateOutputFileLine line \ "Enter output pdb file name for (unsolved) work structure" \ "Work PDB out" \ XYZOUT DIR_XYZOUT #----------------------------------------------------- OpenFolder 1 open CreateLine line \ message "Correct any anisotropy in the input data" \ help anisotropy-correction \ widget DOANIS -width 4 \ label "Apply anisotropy correction to input data." CreateLine line \ message "Build Selenomethionine residues instead of methionine" \ help build-semet \ widget DOSEMET -width 4 \ label "Build Selenomethionine " \ label "(MSE instead of MET)." -italic CreateLine line \ message "Fix the position of the model in the ASU" \ help fix-position \ widget DOFIXPOS -width 4 \ label "Build the new model in the same place as the input model." \ toggle_display USEXYZIN open 1 CreateLine line \ label "Calculation options:" -italic \ CreateLine line \ message "Use fastest rather than best methods (2-3x faster, ~5%% less model)" \ help fast \ widget DOFAST -width 4 \ label "Use fastest rather than best methods." CreateLine line \ message "Number of cycles of building to run" \ help cycles \ label "Number of cycles of building to run:" \ widget NCYCLE -width 4 #----------------------------------------------------- OpenFolder 2 closed CreateLine line \ message "Select how you want to use buccaneer." \ label "Use buccaneer to:" CreateLineTemplate OPTIONS { 0.00 0.025 0.50 0.525 } CreateLine line \ message "Find initial candidate C-alphas by 6D search in the density." \ help grow \ widget DOFIND -width 4 \ label " 1. Find initial candidate C-alphas in the density." \ message "Inserts or deletes residues if there is a sequence mismatch." \ help correct \ widget DOCORCT -width 4 \ label " 6. Correct by rebuilding sequence register errors." \ format template OPTIONS CreateLine line \ message "Grow the candidate C-alphas into chain fragments." \ help grow \ widget DOGROW -width 4 \ label " 2. Grow candidate C-alphas into chain fragments." \ message "Eliminates residues in low density or sequence breaks." \ help filter \ widget DOFILTR -width 4 \ label " 7. Filter out residues for which density is poor." \ format template OPTIONS CreateLine line \ message "Join the chain fragments together by merging overlaps." \ help join \ widget DOJOIN -width 4 \ label " 3. Join the chain fragments together." \ message "Improved model completeness when NCS is present." \ help ncsbuild \ widget DONCSRB -width 4 \ label " 8. Use NCS to rebuild and complete related chains." \ format template OPTIONS CreateLine line \ message "Use loop fitting to try and link nearby N and C terminii." \ help link \ widget DOLINK -width 4 \ label " 4. Link nearby fragments." \ message "Prune any clashing chains." \ help prune \ widget DOPRUNE -width 4 \ label " 9. Prune any clashing chains." \ format template OPTIONS CreateLine line \ message "Matches side chain density against the actual sequence." \ help sequence \ widget DOSEQNC -width 4 \ label " 5. Assign a sequence to the best chains." \ message "Without rebuilding, only N,CA,C atoms are output." \ help build \ widget DOBUILD -width 4 \ label "10. Rebuild side chains and Carbonyl Oxygens." \ format template OPTIONS #----------------------------------------------------- OpenFolder 3 closed CreateLine line \ message "Use correlation mode for completion after MR or initial build" \ help correlation-mode \ widget USECORR -width 4 \ label "Use correlation target function " \ label "(use after MR or for model completion)" -italic CreateLine line \ message "Sequence docking can be cautious, pragmatic, or reckless" \ help sequence-reliability \ label "Assign sequence when a " \ widget SEQREL \ label " match is found." CreateLine line \ message "Select principle secondary structure type." \ help ramachandran-filter \ label "Find secondary structure features preferentially: " \ widget RAMAFLT CreateLine line \ message "Using data beyond 2.0A is slow and seldom helps. (No effect if data resolution is lower than this limit.)" \ help resolution \ label "Truncate data beyond resolution limit/Angstroms:" \ widget RESOLUTION_MAX -width 4 CreateLine line \ message "Number of fragments to build per 100 residues" \ help fragments-per-100-residues \ label "Number of fragments to build per 100 residues:" \ widget NFRAGR -width 4 CreateLine line \ message "Maximum number of fragments to build" \ help fragments \ label "Maximum number of fragments to build:" \ widget NFRAGS -width 4 CreateLine line \ message "Grown residues will be give this residue name in the output." \ label "Residue name for unsequenced residues:" \ widget NEWRESNM -width 4 CreateLine line \ label "Data for (solved) reference structure:" -italic CreateLine line \ message "The default is a good choice." \ label "Library reference structure to use: " \ widget REFCODE \ label " (unless user-defined)." CreateLine line \ message "Select this if you want to use your own reference structure data for an unusual problem." \ widget REFUSER -width 4 \ label "Specify a user-defined reference structure instead of the standard library." OpenSubFrame refin \ -toggle_display REFUSER open 1 CreateInputFileLine line \ "Enter input pdb file name for (solved) reference structure" \ "Reference PDB in" \ XYZINref DIR_XYZINref CreateInputFileLine line \ "Enter input MTZ file name for (solved) reference structure" \ "Reference MTZ in" \ HKLINref DIR_HKLINref \ CreateLabinLine line \ "Observed amplitude (FP) and obligatory sigma (SIGFP)" \ HKLINref "FP" FPref [list FP.F_sigF.F FP ] \ -sigma "SIGFP" SIGFPref [list FP.F_sigF.sigF SIGFP] CreateLabinLine4 line \ "Choose Hendrickson-Lattman coefficients from final model" \ HKLINref "HLA" HLAref [list FC.ABCD.A HLA] \ -dependent "HLB" HLBref [list FC.ABCD.B HLB] \ -dependent "HLC" HLCref [list FC.ABCD.C HLC] \ -dependent "HLD" HLDref [list FC.ABCD.D HLD] CloseSubFrame }