# # Copyright (C) 1999-2004 Liz Potterton, Peter Briggs # # This code is distributed under the terms and conditions of the # CCP4 Program Suite Licence Agreement as a CCP4 Library. # A copy of the CCP4 licence can be obtained by writing to the # CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. # #CCP4i_cvs_Id $Id$ # ====================================================================== # solomon.tcl -- # # Template for task interface # # CCP4Interface # # ======================================================================= #--------------------------------------------------------------------- proc solomon_setup { typedefVar arrayname } { #--------------------------------------------------------------------- upvar #0 $typedefVar typedef global dependentdef set typedef(_solomon_mode) {menu { "flipping" \ "flattening" } { FLIPPING FLATTENING } } set dependentdef(solomon_multiplier) { { flipping flattening } { 1 0 } { -0.75 -1.0 0.0 0.0 } } return 1 } # procedure run before script is written #---------------------------------------------------------------------------- proc solomon_run { arrayname } { #---------------------------------------------------------------------------- upvar #0 $arrayname array # puts "solomon_run EXTEND_RESOLUTION $array(EXTEND_RESOLUTION)" if { $array(EXTEND_RESOLUTION) } { # check we've got some resolution parameters otherwise liable to bomb out later if { $array(INITIAL_RESOLUTION) == "" || $array(FINAL_RESOLUTION) == "" } { WarningMessage \ "You must enter values for initial and final resolution. Job will not be run. Please reset parameters and try again." return 0 } # Check that resolution extension is reasonable set extend_range \ [expr $array(INITIAL_RESOLUTION) - $array(FINAL_RESOLUTION) ] if { $extend_range > $array(MAXIMUM_EXTENSION) } { WarningMessage \ "Attempting to extend resolution > $array(MAXIMUM_EXTENSION) Angstrom is not reasonable. Job will not be run. Please reset parameters and try again." return 0 } set extend_cycles [expr round ($extend_range * 10.0) ] set min_cycles [expr $extend_cycles + 6 ] if { $array(NCYCLES) < $min_cycles } { WarningMessage "Increasing number of cycles to $min_cycles to allow for phase extension" set array(NCYCLES) $min_cycles } else { set extend_cycles [ expr $array(NCYCLES) - 6 ] } set extend_step [expr $extend_range / $extend_cycles ] # puts "extend_cycles $extend_cycles extend_step $extend_step" for { set i 1 } { $i <= 3 } { incr i } { set array(RESOLUTION,$i) $array(INITIAL_RESOLUTION) } for { set i 1 } { $i <= $extend_cycles } { incr i } { set ii [expr $i + 3 ] set array(RESOLUTION,$ii) \ [expr $array(INITIAL_RESOLUTION) - ($i * $extend_step)] } for { set i [expr $extend_cycles +4] } {$i <= $array(NCYCLES) } { incr i } { set array(RESOLUTION,$i) $array(FINAL_RESOLUTION) } } else { # not extending resolution for { set i 1 } { $i <= $array(NCYCLES) } { incr i } { set array(RESOLUTION,$i) $array(INITIAL_RESOLUTION) } } return 1 } #------------------------------------------------------------------ proc solomon_multiplier { arrayname } { #------------------------------------------------------------------ upvar #0 $arrayname array set array(SOLVENT_MULTIPLIER) "" # SOLOMON_MODE AUTO_SCALING } #=CREATE=WINDOW=AND=SUBWINDOWS=========================================== proc solomon_task_window { arrayname } { upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "Run Solomon - Density Modification" "Solomon" \ [ list "Required Parameters" \ "Infrequently Used Options" ] ] == 0 } return SetDefaultMapFormat $arrayname MAPOUT_FORMAT #=PROTOCOL============================================================== OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ message "Generate map" \ widget IFMAPOUT \ label "Create map file in" \ widget MAPOUT_FORMAT \ label "format" #=FILES================================================================ OpenFolder file CreateInputFileLine line \ "Enter input MTZ file name (HKLIN)" \ "MTZ in" \ HKLIN DIR_HKLIN \ -fileout HKLOUT DIR_HKLOUT _solomon \ -setfileparam resolution_max FINAL_RESOLUTION \ -setfileparam resolution_min EXCLUDE_RESOLUTION_MIN CreateLabinLine line \ "Choose amplitude (FO) and OBLIGATORY sigma (SIGFO)" \ HKLIN "FO " FO {FP F_P FOBS} \ -sigma "Sigma " SIGFO {SIGFP SIGP SIG_FP SIG_OBS} CreateLabinLine line \ "Choose phase (PHIIN) and OBLIGATORY weight (WIN)" \ HKLIN "PHIIN " PHIIN {NULL} \ -sigma "Weight" WIN {NULL} CreateOutputFileLine line \ "Enter output MTZ file name or click file browser icon (HKLOUT)" \ "MTZ out" \ HKLOUT DIR_HKLOUT #=PARAMETERS========================================================== OpenFolder 1 CreateLine line \ message "Enter fraction of unit cell volume which is solvent (SLVFRC)" \ help slvfrc \ label "Fraction of solvent in unit cell" \ widget SOLVENT_FRACTION \ -oblig CreateLine line \ message "Choose solvent flattening or flipping (MULSOLV (AUTO))" \ help mulsolv \ widget AUTO_SCALING \ -command "solomon_multiplier $arrayname" \ label "Auto refine multiplier in solvent" \ widget SOLOMON_MODE \ -command "solomon_multiplier $arrayname" \ label "mode" SetProgramHelpFile sfall CreateLine line \ message "Choose to extend resolution (SFALL RESOLUTION)" \ help resolution \ widget EXTEND_RESOLUTION \ label "Extend resolution from" \ widget INITIAL_RESOLUTION \ -oblig \ label "to" \ widget FINAL_RESOLUTION \ -oblig \ message "Choose number of cycles of refinement" \ label "over" \ widget NCYCLES \ label "cycles of refinement" CreateLine line \ message "Use to data to minimum resolution cutoff" \ label "Minimum resolution cutoff" \ widget EXCLUDE_RESOLUTION_MIN CreateLine line \ message "Run in P1 for spacegroups not covered by FFT and Sfall" \ help space_groups \ widget RUN_IN_P1 \ label "Use P1 spacegroup and map for whole cell" #=Unusual parameters================================================================ OpenFolder 2 closed SetProgramHelpFile solomon CreateLine line \ message "Choose to truncate map for extremes of protein density range (TRUNC)" \ help trunc \ label "Truncate protein density for regions below " \ widget TRUNCATE_MIN \ label "or above" \ widget TRUNCATE_MAX \ label "of density range" CreateLine line \ message "Reconstruct low resolution SFs (EXTRUDE & PTOS)" \ help extrude \ widget EXTRUDE_MODE \ -toggleon \ label "Reconstruct low resolution SFs assuming mean protein/solvent density"\ help ptos \ widget DENSITY_RATIO CreateLine line \ message "Solvent analysis - use solvent radius (RADIUS)" \ help radius \ label "Solvent analysis radius" \ widget SOLVENT_RADIUS SetProgramHelpFile fft CreateLine line \ message "Use fixed grid for all generated maps" \ help grid \ widget GRID \ -toggleon \ label "Use fixed grid for all maps nx=" \ widget GRID_1 \ label " ny=" \ widget GRID_2 \ label " nz=" \ widget GRID_3 } #=END=======================================================================