# ====================================================================== # pirate.tcl -- # # CCP4Interface # # ======================================================================= #------------------------------------------------------------------------------ proc pirate_prereq { } { #------------------------------------------------------------------------------ if { ![file exists [FindExecutable cpirate]] } { return 0 } return 1 } #------------------------------------------------------------------------------ proc pirate_run { arrayname } { #------------------------------------------------------------------------------ upvar #0 $arrayname array global env 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(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" } return 1 } #--------------------------------------------------------------------- proc pirate_task_window { arrayname } { #--------------------------------------------------------------------- upvar #0 $arrayname array if { [ CreateTaskWindow $arrayname \ "Phase improvement using Pirate" "Pirate" \ [ list \ "Options" \ "Likelihood Weighting and Bias" \ "Other options" \ ] ] == 0 } return # Set the name of the CCP4 program help file to use SetProgramHelpFile "cpirate" #=PROTOCOL============================================================== OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ message "Use NCS relationships from heavy atoms for phase improvement" \ widget NCSHA -width 4 \ label "Use Non-crystallographic symmetry (NCS)." #=FILES================================================================ OpenFolder file CreateLine line \ label "Data for (solved) reference structure" -italic 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 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 CreateLine line \ label "Data for (unsolved) work structure" -italic CreateInputFileLine line \ "Enter input MTZ file name for (unsolved) work structure" \ "Work MTZ in" \ HKLINwrk DIR_HKLINwrk \ -fileout HKLOUT DIR_HKLOUT "_pirate" 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 phasing" \ HKLINwrk "HLA" HLAwrk [list HLA FC.ABCD.A] \ -dependent "HLB" HLBwrk [list HLB FC.ABCD.B] \ -dependent "HLC" HLCwrk [list HLC FC.ABCD.C] \ -dependent "HLD" HLDwrk [list HLD FC.ABCD.D] CreateLabinLine line \ "Choose Free-R flag" \ HKLINwrk "Free-R flag" FREEwrk [list FreeR_flag] OpenSubFrame pdbinha \ -toggle_display NCSHA open 1 CreateInputFileLine line \ "Enter input heavy-atom PDB file name" \ "Heavy atom PDB file" \ PDBINha DIR_PDBINha CloseSubFrame CreateOutputFileLine line \ "Output MTZ File for results" \ "Work MTZ out" \ HKLOUT DIR_HKLOUT CreateLine line \ message "Output column label prefix (colout)" \ help colout \ label "Output column label prefix" \ widget COLOUT -width 12 #----------------------------------------------------- OpenFolder 1 open CreateLine line \ message "Automatically adjust the content of the unit cell (auto-content)" \ help auto-content \ widget AUTOCONT -width 4 \ label "Perform automatic cell content estimation." \ label " Matches reference structure cell content to work." -italic CreateLine line \ message "Positive values increase specified region of reference, negative decrease. (-1.0...1.0)" \ help evaluate \ label " Skew content of:" \ label " Dense regions" \ widget SKEWCONT1 -width 4 \ label " Ordered regions" \ widget SKEWCONT2 -width 4 \ label " +ve to increase region, -ve to decrease." -italic \ toggle_display AUTOCONT open 0 CreateLine line \ message "Automatically weight the histogram data" \ help auto-mapllk \ widget AUTOMAPW -width 4 \ label "Perform automatic weighting of non-ncs phase information." \ label " Try changing this only if resulting map is poor." -italic CreateLine line \ message "Weight for map likelihood (weight-mapllk)" \ help weight-mapllk \ label "Weight for map likelihood:" \ widget WTMAPLLK -width 4 \ toggle_display AUTOMAPW open 0 OpenSubFrame frame \ -toggle_display NCSHA open 1 CreateLine line \ message "Automatically weight the ncs data" \ help auto-ncsllk \ widget AUTONCSW -width 4 \ label "Perform automatic weighting of ncs phase information." \ label " Try changing this only if resulting map is poor." -italic CreateLine line \ message "Weight for ncs likelihood (weight-ncsllk)" \ help weight-ncsllk \ label "Weight for ncs likelihood:" \ widget WTNCSLLK -width 4 \ toggle_display AUTONCSW open 0 CreateLine line \ message "Select this if you have high order mixed non-crystallographic and crystallographic symmetry" \ label "NCS virus mode" \ widget NCSVIRUS -width 4 \ label " Select this to look for huge NCS related regions." -italic CloseSubFrame #----------------------------------------------------- OpenFolder 2 closed CreateLine line \ message "Use unbias mode to remove bias (biasmode)" \ help biasmode \ widget UNBIAS -width 4 \ label "Use unbias mode to remove bias:" \ label " Useful for molecular replacement." -italic CreateLine line \ message "Use strict Free-R over multiple cycles (strict-free)" \ help strict-free \ widget STRICTFR -width 4 \ label "Use strict Free-R throughout:" \ label " Use this only if refining against output phases." -italic CreateLine line \ message "Weight to correct distributions from phasing (weight-expllk)" \ help weight-expllk \ label "Weight for input phasing: " \ widget WTEXPLLK -width 4 \ label " Use this to correct for flaws in phasing programs." -italic #----------------------------------------------------- OpenFolder 3 closed CreateLine line \ message "Use evaluation mode to evaluate test structures (evaluate)" \ help evaluate \ widget EVALUATE -width 4 \ label "Use evaluation mode." \ label " Does a quick calculation with no output for evaluation of settings." -italic CreateLine line \ message "Number of cycles of refinement (ncycles)" \ help ncycles \ label "Number of cycles:" \ widget NCYCLES -width 3 \ label " Should not make much difference." -italic CreateLine line \ message "Local map filter radius (radius)" \ help radius \ label "Local map filter radius:" \ label " Initial cycle" \ widget RADIUS1 -width 4 \ label " Final cycle" \ widget RADIUS2 -width 4 \ label " The default values are good for most tasks." -italic }