# # 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 $Id$ # ====================================================================== # dmmulti.tcl -- # # Rum DMMulti # # CCP4Interface # # ======================================================================= #-------------------------------------------------------------------- proc dmmulti_setup { typedefVar arrayname } { #-------------------------------------------------------------------- upvar #0 $typedefVar typedef set typedef(_dm_phase_comb) {menu { "omit" \ "perturbation" } { OMIT "PERT" } } set typedef(_dm_scheme) { menu { "automated phase extension" "phase extension in resolution steps" "phase extension in magnitude steps" "phase extension in FOM steps" } { AUTO RES MAG FOM } } set typedef(_dm_wang_mode) { menu { "constant" "w=1-(r/R) Wang's method" "w=1-(r/R)**2" } { 0 1 2 } } set typedef(_dm_skel_cycles) { int 3 2 100 NOTOBLIG {} } set typedef(_dm_ncs_nops) { int 3 1 12 NOTOBLIG {} } set typedef(_dm_ndomains) { int 3 0 6 NOTOBLIG {} } set typedef(_dm_vuout_format) { menu { O XtalView } { vu odat } } set typedef(_dmmulti_dom_menu) { varmenu DMMULTI_DOM_MENU 1 3 } set typedef(_dm_ncross) { menu { "changing random set of hkl" "fixed set of hkl run separately" "multiple free-R sets" } { RANDOM FIXED MULTI } } return 1 } #-------------------------------------------------------------------- proc dmmulti_run { arrayname } { #-------------------------------------------------------------------- upvar #0 $arrayname array set array(INPUT_FILES) "" set array(OUTPUT_FILES) "" for { set n 1 } { $n <= $array(NCRYSTALS) } { incr n } { if $array(SOLVENT_MASK_MODE,$n) { append array(INPUT_FILES) "HKLIN,$n SOLIN,$n " append array(OUTPUT_FILES) "HKLOUT,$n " } else { append array(INPUT_FILES) "HKLIN,$n " append array(OUTPUT_FILES) "HKLOUT,$n SOLOUT,$n " } set array(LABIN,$n) "FP SIGFP PHIO FOMO" set array(LABOUT,$n) "PHIDM FOMDM" if { $array(USE_HL,$n) } { append array(LABIN,$n) " HLA HLB HLC HLD" # append array(LABOUT,$n) " HLADM HLBDM HLCDM HLDDM" } } for { set n 1 } { $n <= $array(NDOMAINS) } { incr n } { if { [file exists [GetFullFileName0 $arrayname MASKIN,$n]] } { append array(INPUT_FILES) "MASKIN,$n " } } set id $array(LABOUT_ID) set array(PHIDM) "PHI$id" set array(FOMDM) "FOM$id" set array(HLADM) "HLA$id" set array(HLBDM) "HLB$id" set array(HLCDM) "HLC$id" set array(HLDDM) "HLD$id" return 1 } #====================================================================== proc DmDomainFrame { arrayname counter } { #====================================================================== upvar #0 $arrayname array # update the variable menu used in the xtal definitions if { $counter == 1 } { set mode initialise } else { set mode append } UpdateVariableMenu $arrayname $mode $counter DMMULTI_DOM_MENU $counter CreateInputFileLine line \ "Enter name of optional domain mask file " \ "Domain mask" \ MASKIN DIR_MASKIN \ -help files \ -toggle_display NCSMASK hide 1 \ -notoblig } # ================================================================== proc DmDomainOpsFrame { arrayname counter domain } { # ================================================================== upvar #0 $arrayname array # puts "DmDomainOpsFrame domain $domain" if { $counter == 1 && $domain == 1 } { set array(NCS_OP_DOM,1_$counter) 1 set array(NCS_OP_ALPHA,1_$counter) 0.0 set array(NCS_OP_BETA,1_$counter) 0.0 set array(NCS_OP_GAMMA,1_$counter) 0.0 set array(NCS_OP_XTRAN,1_$counter) 0.0 set array(NCS_OP_YTRAN,1_$counter) 0.0 set array(NCS_OP_ZTRAN,1_$counter) 0.0 } CreateLine ops_frame \ message "Enter Averaging Operator (ROTA EULER & TRAN)" \ help average \ widget NCS_OP_DOM \ widget NCS_OP_ALPHA -oblig \ widget NCS_OP_BETA -oblig \ widget NCS_OP_GAMMA -oblig \ widget NCS_OP_XTRAN -oblig \ widget NCS_OP_YTRAN -oblig \ widget NCS_OP_ZTRAN -oblig \ format template NCSOPS } #---------------------------------------------------------------- proc DmCrystalFrame { arrayname counter } { #---------------------------------------------------------------- CreateLine line \ label "Crystal number $counter" -italic CreateLine line \ message "Use pre-determined solvent mask (SOLIN) " \ help files \ widget SOLVENT_MASK_MODE \ label "Input a solvent mask " \ help labin \ widget USE_HL \ label "Input Hendrickson-Lattman coefficients" CreateInputFileLine line \ "Enter input MTZ file name (HKLIN$counter)" \ "MTZ in" \ HKLIN DIR_HKLIN \ -help files \ -fileout HKLOUT,$counter DIR_HKLOUT,$counter "_dmmulti" \ -fileout SOLOUT,$counter DIR_SOLOUT,$counter "_dmmulti" CreateLabinLine line \ "Choose amplitude (FP) and essential sigma (SIGFP)" \ HKLIN,$counter "FP" FP {} \ -sigma "SIGFP" SIGFP {} \ -help labin CreateLabinLine line \ "Choose phase (PHIO) and essential weighting factor (FOMO)" \ HKLIN,$counter "PHIO" PHIO {} \ -sigma "Weight" FOMO {} \ -help labin OpenSubFrame frame \ -toggle_display USE_HL,$counter open 1 CreateLabinLine line \ "Choose Hendrickson-Lattman coefficients" \ HKLIN,$counter "HLA" HLA HLA\ -sigma "HLB" HLB HLB \ -help labin CreateLabinLine line \ "Choose Hendrickson-Lattman coefficients" \ HKLIN,$counter "HLC" HLC HLC\ -sigma "HLD" HLD HLD \ -help labin CloseSubFrame CreateOutputFileLine line \ "Enter name of output MTZ file (HKLOUT$counter)" \ "MTZ out" \ HKLOUT DIR_HKLOUT \ -help files CreateInputFileLine line \ "Enter name of input solvent mask file (SOLIN$counter)" \ "Solvent in" \ SOLIN DIR_SOLIN \ -help files \ -toggle_display SOLVENT_MASK_MODE,$counter hide 0 CreateOutputFileLine line \ "Enter name of output solvent mask file (SOLOUT$counter)" \ "Solvent out" \ SOLOUT DIR_SOLOUT \ -toggle_display SOLVENT_MASK_MODE,$counter hide 1 \ -help files } #-------------------------------------------------------------------- proc DmSolvent { arrayname counter } { #-------------------------------------------------------------------- CreateLine line \ label "Describe Crystal $counter" -italic CreateLine line \ message "Set maximum range of the phase extension (RESOLUTION)" \ help resolution \ label "Use reflections in range" \ widget RESOLUTION_MIN \ label to \ widget RESOLUTION_MAX \ CreateLine line \ message "Fraction of unit cell which is solvent (SOLC)" \ help solc \ label "Fraction solvent content" \ widget SOLVENT_FRAC -oblig CreateLine line \ widget XTAL_REFINE_OP \ label "Refine the averaging operators for this crystal" CreateLine line \ help average \ label domain -italic \ label "alpha" -italic \ label "beta" -italic \ label "gamma" -italic \ label "xtran" -italic \ label "ytran" -italic \ label "ztran" -italic \ format template NCSOPS CreateExtendingFrame NCS_NOPS DmDomainOpsFrame \ "Add/remove line to define extra averaging operator" \ "Add operator" \ [ list NCS_OP_DOM \ NCS_OP_ALPHA \ NCS_OP_BETA \ NCS_OP_GAMMA \ NCS_OP_XTRAN \ NCS_OP_YTRAN \ NCS_OP_ZTRAN ] \ -counter $counter } #-------------------------------------------------------------------- proc DmSolventMasks { arrayname counter } { #-------------------------------------------------------------------- CreateLine line \ label "Creating solvent mask for crystal $counter" -italic CreateLine line \ message "Set alternative mask volumes for histogram matching and solvent flattening" \ help solc_mask \ label "Histogram and solvent flattening mask solvent fraction" \ widget SOLC_MASK_SOLV \ label "and protein fraction" \ widget SOLC_MASK_PROT CreateLine line \ message "Set mean density for solvent and protein regions(SOLC MEAN)" \ label "Mean density of solvent" \ help solc_mean \ widget SOLC_MEAN_SOLVVAL \ label "and protein" \ widget SOLC_MEAN_PROTVAL } #-------------------------------------------------------------------- proc dmmulti_task_window {arrayname} { #-------------------------------------------------------------------- upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "Run DmMulti - Multi-Crystal Density Modification" "DmMulti" \ [list "Describe Domains" \ "Describe Crystals" \ "Solvent Mask Options" \ "Infrequently Used Parameters" ] ] == 0 } return # WriteCredits [list {Kevin Cowtan}] -link "Kevin's Home Page" \ # "http://www.ysbl.york.ac.uk/~cowtan" SetDefaultMapFormat $arrayname MAPOUT_FORMAT CreateLineTemplate NCSOPS [list 0.0 0.10 0.25 0.40 0.55 0.70 0.85] CreateLineTemplate NCSREF [list 0.0 0.6 0.65] #=PROTOCOL============================================================== OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ message "Choose the mode(s) of density modification (MODE)" \ label "Select density modification modes" \ -italic CreateLine line \ message "Choose the mode(s) of density modification (MODE)" \ help mode \ widget DM_SOLVENT \ label "Solvent" \ widget DM_HISTOGRAM \ label "Histogram" \ widget DM_AVERAGING \ label Averaging CreateLine line \ message "Choose phase extension scheme (SCHEME)" \ help scheme \ label Do \ widget DM_SCHEME \ toggle_display DM_SCHEME open AUTO CreateLine line \ message "Choose phase extension scheme (SCHEME)" \ help scheme_res \ label Do \ widget DM_SCHEME \ label "starting at resolution" \ widget DM_SCHEME_RES -oblig \ toggle_display DM_SCHEME open RES CreateLine line \ message "Choose phase extension scheme (SCHEME)" \ help scheme_frac \ label Do \ widget DM_SCHEME \ label "starting with " \ widget DM_SCHEME_FRAC -oblig \ label "fraction of reflections" \ toggle_display DM_SCHEME hide [list RES AUTO] CreateLine line \ message "Number of cycles of phase extension (NCYCLE)" \ help ncycle \ label Do \ widget DM_NCYCLES \ label "cycles of phase extension using FreeR set:" \ widget DM_NCROSS_MODE \ widget DM_NCROSS_NSETS \ toggle_display DM_NCROSS_MODE open MULTI CreateLine line \ message "Number of cycles of phase extension (NCYCLE)" \ help ncycle \ label Do \ widget DM_NCYCLES \ label "cycles of phase extension using FreeR set:" \ widget DM_NCROSS_MODE \ toggle_display DM_NCROSS_MODE hide MULTI CreateLine line \ message "Enter text for output label (eg entering 'DM' gives output labels 'FDM' etc)" \ help labout \ label "Output label identifier" \ widget LABOUT_ID #=FILES================================================================ OpenFolder file CreateExtendingFrame NCRYSTALS DmCrystalFrame \ "Enter names of one MTZ file per crystal" \ "Add MTZ File" \ [ list HKLIN DIR_HKLIN HKLOUT DIR_HKLOUT SOLIN DIR_SOLIN \ SOLOUT DIR_SOLOUT SOLVENT_MASK_MODE USE_HL \ LABIN FP SIGFP PHIO FOMO HLA HLB HLC HLD ] \ -dependentframe DmSolvent \ -dependentframe DmSolventMasks #----------------------------------------------------------Domain definitions OpenFolder 1 CreateToggleFrame NDOMAINS DmDomainFrame \ "Open another domain frame" "Domain number" \ "Add domain" \ [list MASKIN \ DIR_MASKIN ] #----------------------------------------------------------Xtal definitions OpenFolder 2 CreateExtendingFrame NCRYSTALS DmSolvent \ "Solvent content of each crystal" \ " " [list SOLVENT_FRAC SOLC_MASK_SOLV SOLC_MASK_PROT \ SOLC_MEAN_PROTVAL SOLC_MEAN_SOLVVAL \ RESOLUTION_MIN RESOLUTION_MAX XTAL_REFINE_OP NCS_NOPS ] -noaddline \ -child DmDomainOpsFrame #--------------------------------------------------------------Solvent mask OpenFolder 3 DM_SOLVENT closed 1 hide CreateLine line \ message "Default enter no radius and program will derive value" \ help wang \ label "Use Wang with radius" \ widget WANG_RADIUS \ label "and weighting scheme" \ widget WANG_MODE CreateLine line \ message "Set a rho max to truncate heavy atoms" \ help wang \ label "set rho cutoffs, minimum" \ widget WANG_RHO_MIN \ label maximum \ widget WANG_RHO_MAX CreateExtendingFrame NCRYSTALS DmSolventMasks \ "Creating solvent masks" \ " " [list SOLC_MASK_SOLV SOLC_MASK_PROT \ SOLC_MEAN_PROTVAL SOLC_MEAN_SOLVVAL ] \ -noaddline #------------------------------------------------------------------Infrequent OpenFolder 4 closed CreateLine line \ message "NOT recommended to override the scale! (SCALE)" \ help scale \ label "Overide internal scaling for histogram maps, Bfactor" \ widget SCALE_BFAC \ label "and scale" \ widget SCALE_SCALE CreateLine line \ message "Use non-default map grid (GRID)" \ help grid \ widget GRID \ -toggleon \ label "Map grid nx"\ widget GRID_1 \ label "ny" \ widget GRID_2 \ label "nz" \ widget GRID_3 }