# # 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 $Id$ # ====================================================================== # sigmaa.tcl -- # # CCP4Interface # # ====================================================================== #----------------------------------------------------------------------- proc sigmaa_setup { typedefVar arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array upvar #0 $typedefVar typedef set typedef(_sigmaa_calc_type) {menu { \ "phase using partial structure information" \ "combine isomorphous phase with partial structure" \ "combine two sets of MIR phases" } \ { PART COMB_PART COMB_MIR } } return 1 } #----------------------------------------------------------------------- proc sigmaa_nps_labout { arrayname counter } { #----------------------------------------------------------------------- if {$counter > 2 } { set array(NPS) 2 return } CreateLabinLine line \ "Computed amplitude (FC) and sigma (PHIC)" \ HKLIN Fcalc FCN FCN \ -sigma Phase PHICN PHICN CreateLine line \ message "default value 1.0" \ label "Damping for additional partial structure" \ widget DAMPN } #----------------------------------------------------------------------- proc sigmaa_task_window { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "Improved Fourier coefficients using calculated phases" "Sigmaa" \ [ list "Additional Partial Structures" \ "Program Parameters" \ "Output MTZ Column Labels" \ "Output and monitoring" \ ] ] == 0 } return SetProgramHelpFile sigmaa #=PROTOCOL============================================================== OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ label "Combination required " \ widget SIGMAA_ACTION CreateLine line \ widget USE_HL \ label "Input Hendrickson-Lattman coefficients" \ toggle_display SIGMAA_ACTION open [list COMB_PART COMB_MIR] CreateLine line \ widget USE_SFALL \ label "Generate structure factors using SFALL" \ toggle_display SIGMAA_ACTION open [list PART COMB_PART] #=FILES================================================================ OpenFolder file CreateInputFileLine line \ "Enter input MTZ file name (HKLIN)" \ "MTZ in" \ HKLIN DIR_HKLIN \ -setfileparam space_group_name SIGMAA_SPACE_GROUP \ -setfileparam resolution_min RESOLUTION_MIN \ -setfileparam resolution_max RESOLUTION_MAX \ -setfileparam cell CELL \ -fileout HKLOUT DIR_HKLOUT _sigmaa CreateLabinLine line \ "Choose amplitude (FP) and sigma (SIGFP)" \ HKLIN FP FP FP \ -sigma Sigma SIGFP SIGFP OpenSubFrame frame -toggle_display SIGMAA_ACTION open COMB_PART CreateLabinLine line \ "MIR phase (PHIBP) and weight (WP)" \ HKLIN PHIBP PHIBP PHIBP \ -sigma FoM WP WP \ OpenSubFrame frame -toggle_display USE_HL open 1 CreateLabinLine line \ "Hendrickson-Lattman probability coeffs." \ HKLIN A HLA HLA \ -sigma B HLB HLB CreateLabinLine line \ "Hendrickson-Lattman probability coeffs." \ HKLIN C HLC HLC \ -sigma D HLD HLD CloseSubFrame CloseSubFrame OpenSubFrame frame -toggle_display SIGMAA_ACTION open [list PART COMB_PART] CreateLabinLine line \ "Computed amplitude (FC) and sigma (PHIC)" \ HKLIN Fcalc FC FC \ -sigma Phase PHIC PHIC \ -toggle_display USE_SFALL open 0 CreateLabinLine line \ "Choose Free R column data (LABIN FREER)" \ HKLIN FreeR FREE [list FREE FreeR FreeR_flag] OpenSubFrame frame -toggle_display USE_SFALL open 1 CreateInputFileLine line \ "Enter input coordinate file name (XYZIN)" \ "PDB in" \ XYZIN DIR_XYZIN \ CreateLaboutLine line \ "Enter names for output column labels for calculated Fs and PHIs (LABOUT)"\ HKLOUT Fcalc SFALL_FC \ -sigma PHIcalc SFALL_PHIC CloseSubFrame CloseSubFrame OpenSubFrame frame -toggle_display SIGMAA_ACTION open COMB_MIR CreateLine line \ label "Data for first MIR phases" -italics CreateLabinLine line \ "Centroid phase (PHIBP) and figure of merit (WP)" \ HKLIN "PhiB" PHIBP PHIBP \ -sigma FoM WP WP OpenSubFrame frame -toggle_display USE_HL open 1 CreateLabinLine line \ "Hendrickson-Lattman probability coeffs." \ HKLIN A HLA HLA \ -sigma B HLB HLB CreateLabinLine line \ "Hendrickson-Lattman probability coeffs." \ HKLIN C HLC HLC \ -sigma D HLD HLD CloseSubFrame CreateLine line \ label "Data for second MIR phases" -italics CreateLabinLine line \ "Centroid phase and FoM for second set" \ HKLIN "PhiB" PHIB2 PHIB2 \ -sigma FoM W2 W2 OpenSubFrame frame -toggle_display USE_HL open 1 CreateLabinLine line \ "Hendrickson-Lattman probability coeffs." \ HKLIN A HLA2 HLA2 \ -sigma B HLB2 HLB2 CreateLabinLine line \ "Hendrickson-Lattman probability coeffs." \ HKLIN C HLC2 HLC2 \ -sigma D HLD2 HLD2 CloseSubFrame CloseSubFrame CreateOutputFileLine line \ "Enter name of output file (HKLOUT)" \ "Output" HKLOUT DIR_HKLOUT \ -help notes_on_hklout #=PARAMETERS2========================================================= OpenFolder 1 SIGMAA_ACTION closed COMB_PART hide CreateExtendingFrame NPS sigmaa_nps_labout \ "Partial structures" "Add partial structure (max. 2)" \ [list FCN PHICN DAMPN ] OpenFolder 2 CreateLine line \ message "Exclude reflections below and/or above resolution limit in \ Angstrom (RESOLUTION)" \ help resolution \ widget SIGMAA_RESOLUTION -toggleon \ label "Resolution less than" \ widget RESOLUTION_MIN \ label "A or greater than" \ widget RESOLUTION_MAX \ label "A" CreateLine line \ message "Space group (default as in MTZ file) (SYMMETRY)" \ label "Generate map in space group" \ help symmetry \ widget SIGMAA_SPACE_GROUP CreateLine line \ message "Number of resolution bins (max. 50)" \ label "Number of bins " \ widget RANGES_NBIN OpenSubFrame frame -toggle_display SIGMAA_ACTION open [list COMB_PART PART ] CreateLine line \ message "default value 1.0" \ label "Damping for partial structure" \ widget DAMP CloseSubFrame OpenSubFrame frame -toggle_display USE_SFALL open 1 CreateLine line \ message "Cell dimensions (default from MTZ file) (CELL)" \ help "cell" \ widget IFCELL \ -toggleon \ label "Set cell a" \ 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 CloseSubFrame #===================================================================== OpenFolder 3 closed OpenSubFrame frame -toggle_display SIGMAA_ACTION open PART CreateLaboutLine line \ "Figure of merit m (Sim weight)" \ HKLOUT "FoM " WCMB CreateLaboutLine line \ "Fourier Amplitude for difference map (mFo-DFc)" \ HKLOUT "mF-Df " DELFWT CreateLaboutLine line \ "Fourier Amplitude for 2Fo-Fc map (2mFo-DFc)" \ HKLOUT "2mF-Df " FWT CloseSubFrame OpenSubFrame frame -toggle_display SIGMAA_ACTION open COMB_MIR CreateLaboutLine line \ "Combined phase angle and weight" \ HKLOUT "Phase " PHCMB \ -sigma "FoM " WCMB OpenSubFrame frame -toggle_display USE_HL open 1 CreateLaboutLine line \ "Hendrick-Lattman Coeff" \ HKLOUT "A " HLAC \ -sigma "B " HLBC CreateLaboutLine line \ "Hendrick-Lattman Coeff" \ HKLOUT "C " HLCC \ -sigma "D " HLDC CloseSubFrame CloseSubFrame OpenSubFrame frame -toggle_display SIGMAA_ACTION open COMB_PART CreateLaboutLine line \ "Combined Phase and weight" \ HKLOUT "Phase " PHCMB \ -sigma "FoM " WCMB CreateLaboutLine line \ "Fourier Amplitude for difference map (mFo-DFc) and Phase" \ HKLOUT "mF-Df " DELFWT \ -sigma "Phase " PHDELFWT CreateLaboutLine line \ "Fourier Amplitude for 2Fo-Fc map (2mFo-DFc) and Phase" \ HKLOUT "2mF-Df " FWT \ -sigma "Phase " PHFWT CloseSubFrame #=PARAMETERS3========================================================= OpenFolder 4 closed CreateLine line \ message "Output every nth reflection" \ label "Monitoring interval" \ widget RANGES_MON CreateLine line \ message "Estimate the rms coordinate error" \ widget SIGMAA_ERROR \ label "Undertake error analysis" }