# # 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 $Id$ # ====================================================================== # dm.tcl -- # # Rum DM Density Modification # # CCP4Interface # # ======================================================================= #-------------------------------------------------------------------- proc dm_setup { typedefVar arrayname } { #-------------------------------------------------------------------- upvar #0 $typedefVar typedef set typedef(_dm_phase_comb) {menu { "omit" \ "perturbation" } { OMIT "PERT" } } set typedef(_dm_scheme) { menu { "all reflections" "automated phase extension" "phase extension in resolution steps" "phase extension in magnitude steps" "phase extension in FOM steps" } { ALL 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 30 NOTOBLIG {} } set typedef(_dm_ndomains) { int 3 0 6 NOTOBLIG {} } set typedef(_dm_vuout_format) { menu { O XtalView } { odat vu } } set typedef(_dm_ncs_op_type) { menu { "euler angles" "polar angles" "rotation matrix" "O matrix" } { EULER POLAR MATRIX OMAT } } return 1 } # procedure run before script is written #-------------------------------------------------------------------- proc dm_run { arrayname } { #-------------------------------------------------------------------- upvar #0 $arrayname array if $array(SOLVENT_MASK_MODE) { set array(INPUT_FILES) "HKLIN MASKIN" set array(OUTPUT_FILES) "HKLOUT" } else { set array(INPUT_FILES) "HKLIN" set array(OUTPUT_FILES) "HKLOUT MASKOUT" } set array(LABIN) "FP SIGFP PHIO FOMO" if { $array(USE_HL) } { # Check that the same labels have not been assigned # twice accidentally if { [ DmCheckHLCoeffs $arrayname [ list HLA HLB HLC HLD ] ] == 0 } \ { return 0 } # Add input HL coefficients to LABIN append array(LABIN) " HLA HLB HLC HLD" } set id $array(LABOUT_ID) set array(FDM) "F$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" set array(LABOUT) "FDM PHIDM FOMDM" if { $array(USE_HL) } { append array(LABOUT) " HLADM HLBDM HLCDM HLDDM" } if { $array(IF_SOLMASK_WANG) && $array(WANG_RADIUS) == "" } { set array(WANG_RADIUS) -0.0 } if { $array(SOLMASK_FRAC_SOLV) != "" && $array(SOLMASK_FRAC_PROT) == "" } { set array(SOLMASK_FRAC_PROT) [expr 1.0 - $array(SOLMASK_FRAC_SOLV)] } if { ![SetHarvestParams $arrayname HKLIN -run] } { return 0 } return 1 } #--------------------------------------------------------------------- proc DmCheckHLCoeffs { arrayname labellist } { #--------------------------------------------------------------------- # Procedure to check that the names supplied for input # Hendrickson-Lattman coefficients have been uniquely assigned. If not # then a warning dialogue is issued allowing the user to either proceed # with the non-unique assignments (in which case 1 is returned) \ # or abort the run (0 is returned). # A copy of this procedure also appears in the refmac5 interface. upvar #0 $arrayname array # Check that the same labels have not been assigned # twice accidentally set hl_list "" foreach label $labellist { if { [lsearch $hl_list $array($label)] < 0 } { lappend hl_list $array($label) } } # If the list has less than 4 elements then they were # not all unique if { [llength $hl_list] < 4 } { set action [ChooseOptionDialog "Hendrickson-Lattman Coefficients" "Dm" \ "Labels for the Hendrickson-Lattman coefficients taken from\nthe input file have not been set uniquely\n\nYou can proceed with the current assignments, or abort the run\nand reassign the labels" \ { Abort OK } -default 1 ] if [regexp Abort $action] { return 0 } } return 1 } #====================================================================== proc DmDomainFrame { arrayname counter } { #====================================================================== upvar #0 $arrayname array # puts "DmDomainFrame $counter " CreateInputFileLine line \ "Enter name of optional NCS mask file " \ "NCS mask" \ NCS_MASK_FILE DIR_NCS_MASK_FILE \ help ncsmask \ -toggle_display NCSMASK hide 1 \ -notoblig CreateLineTemplate NCSREF [list 0.0 0.6 0.65] CreateLineTemplate NCSOPS [list 0.05 0.20 0.35 0.50 0.65 0.80] CreateLine line \ message "Refine averaging operator for this mask? (AVERAGE REF)" \ help keywords_averaging \ label "Enter averaging operators below" \ widget NCS_REFINE_OP \ label "Refine averaging operators?" \ format template NCSREF CreateLine line \ label "alpha" -italic \ label "beta" -italic \ label "gamma" -italic \ label "xtran" -italic \ label "ytran" -italic \ label "ztran" -italic \ format template NCSOPS \ toggle_display NCS_OP_TYPE open [list EULER] CreateLine line \ label "omega" -italic \ label "phi" -italic \ label "kappa" -italic \ label "xtran" -italic \ label "ytran" -italic \ label "ztran" -italic \ format template NCSOPS \ toggle_display NCS_OP_TYPE open [list POLAR] CreateLine line \ label "Rotation matrix in CCP4 convention:" -italic \ toggle_display NCS_OP_TYPE open [list MATRIX] CreateLine line \ label "Rotation matrix in O convention (i.e. transposed wrt to CCP4 convention):" -italic \ toggle_display NCS_OP_TYPE open [list OMAT] CreateExtendingFrame NCS_NOPS DmDomainOpsFrame \ "Add line to define extra averaging operator (max 30)" \ "Add operator" \ [ list NCS_OP_ALPHA \ NCS_OP_BETA \ NCS_OP_GAMMA \ NCS_OP_XTRAN \ NCS_OP_YTRAN \ NCS_OP_ZTRAN \ NCS_OP_R11 \ NCS_OP_R12 \ NCS_OP_R13 \ NCS_OP_R21 \ NCS_OP_R22 \ NCS_OP_R23 \ NCS_OP_R31 \ NCS_OP_R32 \ NCS_OP_R33 ] \ -counter $counter } proc dm_phase_comb { arrayname } { upvar #0 $arrayname array if { [GetValue $arrayname PHASE_COMB ] == "OMIT" } { SetValue $arrayname DM_SCHEME ALL set array(DM_NCYCLES_NOT_AUTO) 0 } } # ================================================================== proc DmDomainOpsFrame { arrayname counter domain } { # ================================================================== upvar #0 $arrayname array CreateLineTemplate NCSOPS [list 0.05 0.20 0.35 0.50 0.65 0.80] # puts "DmDomainOpsFrame domain $domain" if { $counter == 1 } { set array(NCS_OP_ALPHA,[subst $domain]_$counter) 0.0 set array(NCS_OP_BETA,[subst $domain]_$counter) 0.0 set array(NCS_OP_GAMMA,[subst $domain]_$counter) 0.0 set array(NCS_OP_XTRAN,[subst $domain]_$counter) 0.0 set array(NCS_OP_YTRAN,[subst $domain]_$counter) 0.0 set array(NCS_OP_ZTRAN,[subst $domain]_$counter) 0.0 set array(NCS_OP_R11,[subst $domain]_$counter) "1.0" set array(NCS_OP_R12,[subst $domain]_$counter) "0.0" set array(NCS_OP_R13,[subst $domain]_$counter) "0.0" set array(NCS_OP_R21,[subst $domain]_$counter) "0.0" set array(NCS_OP_R22,[subst $domain]_$counter) "1.0" set array(NCS_OP_R23,[subst $domain]_$counter) "0.0" set array(NCS_OP_R31,[subst $domain]_$counter) "0.0" set array(NCS_OP_R32,[subst $domain]_$counter) "0.0" set array(NCS_OP_R33,[subst $domain]_$counter) "1.0" } CreateLine ops_frame \ message "Enter Averaging Operator (ROTA EULER/POLAR & TRAN). Translation in Angstrom." \ help keywords_averaging \ 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 \ toggle_display NCS_OP_TYPE open [ list EULER POLAR ] CreateLine ops_frame \ message "Enter Averaging Operator matrix (ROTA MATRIX/OMAT)" \ widget NCS_OP_R11 -oblig \ widget NCS_OP_R12 -oblig \ widget NCS_OP_R13 -oblig \ format template NCSMAT \ toggle_display NCS_OP_TYPE open [ list MATRIX OMAT ] CreateLine ops_frame \ message "Enter Averaging Operator matrix (ROTA MATRIX/OMAT)" \ widget NCS_OP_R21 -oblig \ widget NCS_OP_R22 -oblig \ widget NCS_OP_R23 -oblig \ format template NCSMAT \ toggle_display NCS_OP_TYPE open [ list MATRIX OMAT ] CreateLine ops_frame \ message "Enter Averaging Operator matrix (ROTA MATRIX/OMAT)" \ widget NCS_OP_R31 -oblig \ widget NCS_OP_R32 -oblig \ widget NCS_OP_R33 -oblig \ format template NCSMAT \ toggle_display NCS_OP_TYPE open [ list MATRIX OMAT ] CreateLine line \ message "Enter Averaging Operator translation" \ label "xtran" \ widget NCS_OP_XTRAN -oblig \ label "ytran" \ widget NCS_OP_YTRAN -oblig \ label "ztran" \ widget NCS_OP_ZTRAN -oblig \ format template NCSOPS \ toggle_display NCS_OP_TYPE open [ list MATRIX OMAT ] } #-------------------------------------------------------------------- proc dm_task_window {arrayname} { #-------------------------------------------------------------------- upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "Run DM - Density Modification" "DM" \ [list "Data Harvesting" \ "Required Parameters" \ "Define NCS Symmetry" \ "NCS Averaging" \ "Solvent Mask Options" \ "Infrequently Used Parameters" ] ] == 0 } return SetDefaultMapFormat $arrayname MAPOUT_FORMAT SetHarvestParams $arrayname HKLIN -init #=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" OpenSubFrame frame -toggle_display DM_AVERAGING open 1 CreateLine line \ message "Use automask in NCS averaging" \ help ncsmask \ widget NCSMASK \ label "Automatically generate NCS mask" CreateLine line \ message "Create file containing graphical illustration of the NCS operators" \ widget IFVUOUT \ label "Create file to display NCS operators in" \ widget VUOUT_FORMAT \ label format CloseSubFrame CreateLine line \ message "Phase combination scheme (COMBINE)" \ help combine \ label "Phase combination scheme" \ widget PHASE_COMB \ -command "dm_phase_comb $arrayname" \ label "using" \ widget DM_SCHEME \ toggle_display PHASE_COMB hide OMIT CreateLine line \ message "Phase combination scheme (COMBINE)" \ help combine \ label "Phase combination scheme" \ widget PHASE_COMB \ -command "dm_phase_comb $arrayname" \ label "using all reflections" \ toggle_display PHASE_COMB open OMIT CreateLine line \ message "This option can remove model bias from MR phases if you have NCS" \ help combine_weight \ label "For Molecular Replacement phases:" \ widget NOCOMBINE \ label "Disable phase combination to remove bias." CreateLine line \ message "Use pre-determined solvent mask (SOLIN) " \ help solin \ widget SOLVENT_MASK_MODE \ label "Input a solvent mask " \ message "These may help " \ help labin \ widget USE_HL \ label "Input Hendrickson-Lattman coefficients" \ message "e.g. from Phaser or a previous DM calculation" \ help labin \ widget USE_COEFFS \ label "Input starting map coefficients" CreateLine line \ message "Generate map" \ widget IF_MAPOUT \ -toggleon \ 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 "_dm" \ -fileout MASKOUT DIR_MASKOUT "_dm" \ -setfileparam resolution_min EXCLUDE_RESOLUTION_MIN \ -setfileparam resolution_max EXCLUDE_RESOLUTION_MAX \ -command "UpdateHarvestMTZ $arrayname HKLIN" CreateLabinLine line \ "Choose amplitude (FP) and essential sigma (SIGFP)" \ HKLIN "FP" FP {} \ -sigma "SIGFP" SIGFP {} CreateLabinLine line \ "Choose phase (PHIO) and essential weighting factor (FOMO)" \ HKLIN "PHIO" PHIO {} \ -sigma "Weight" FOMO {} CreateLabinLine4 line \ "Choose Hendrickson-Lattman coefficients (turn off above, if not available)" \ HKLIN "HLA" HLA HLA \ -dependent "HLB" HLB HLB \ -dependent "HLC" HLC HLC \ -dependent "HLD" HLD HLD \ -toggle_display USE_HL open 1 CreateLabinLine line \ "Input map coefficients of the starting map (FDM, PHIDM)" \ HKLIN "FDM" FDMIN {} \ -sigma "PHDM" PHIDMIN {} \ -toggle_display USE_COEFFS open 1 # CreateLabinLine line \ # "Choose FreeR parameter " \ # HKLIN "FreeR" FREER {} \ # -toggle_display PHASE_COMB hide OMIT # CreateOutputFileLine line \ "Enter name of output MTZ file (HKLOUT)" \ "MTZ out" \ HKLOUT DIR_HKLOUT CreateLine line \ message "Enter text for output label (eg entering 'DM' gives output labels 'FDM' etc)" \ label "Output label identifier" \ widget LABOUT_ID CreateInputFileLine line \ "Enter name of input solvent mask file (SOLIN)" \ "Mask in" \ MASKIN DIR_MASKIN \ -help solin \ -toggle_display SOLVENT_MASK_MODE hide 0 CreateOutputFileLine line \ "Enter name of output solvent mask file (SOLOUT)" \ "Mask out" \ MASKOUT DIR_MASKOUT \ -toggle_display SOLVENT_MASK_MODE hide 1 \ -help solout #=PARAMETERS========================================================== OpenFolder 1 CreateHarvestLine line OpenFolder 2 CreateLine line \ message "Fraction of unit cell which is solvent (SOLC)" \ help solc \ label "Fraction solvent content" \ widget SOLVENT_FRAC -oblig CreateLine line \ message "Number of cycles of phase extension (NCYCLE) default is AUTO" \ help ncycle_auto \ widget DM_NCYCLES_NOT_AUTO \ -toggleon \ label "Fix number of cycles of phase extension to" \ help ncycle \ widget DM_NCYCLES \ toggle_display PHASE_COMB hide OMIT CreateLine line \ message "Resolution limit of starting set (SCHEME RES)" \ label "Resolution of starting set in phase extension" \ help scheme_res \ widget DM_SCHEME_RES -oblig \ toggle_display DM_SCHEME open RES CreateLine line \ message "Fraction of reflections in starting set (SCHEME FRAC)" \ label "Fraction of reflections in starting set" \ help scheme_res \ widget DM_SCHEME_FRAC -oblig \ toggle_display DM_SCHEME hide [list RES ALL AUTO] #======================================================================== OpenFolder 3 DM_AVERAGING open 1 hide CreateLine line \ message "Select convention for specifying the NCS operator" \ help average \ label "Define NCS operators in terms of" \ widget NCS_OP_TYPE CreateLineTemplate NCSOPS [list 0.05 0.20 0.35 0.50 0.65 0.80] CreateLineTemplate NCSREF [list 0.0 0.6 0.65] CreateLineTemplate NCSMAT [list 0.0 0.3 0.6 ] CreateToggleFrame NCS_NDOMAINS DmDomainFrame \ "Open another domain frame" "Domain number" \ "Add domain" \ [list NCS_MASK_FILE \ DIR_NCS_MASK_FILE \ NCS_REFINE_OP \ NCS_NOPS ] \ -child DmDomainOpsFrame #======================================================================== OpenFolder 4 DM_AVERAGING open 1 hide CreateLine line \ message "Default computed by program if you do not enter a value(NCSMASK NMER)" \ help ncsmask_nmer \ label "Number of monomers related by proper symmetries" \ widget NCSMASK_NMER CreateLine line \ message "Update the averaging mask every cycles. (NCSMASK UPDATE)" \ help ncsmask \ widget IF_NCSMASK_UPDATE \ -toggleon \ label "Update averaging mask every" \ widget NCSMASK_UPDATE_NCYC \ label "cycles" CreateLine line \ message "Limits on search space over which mask formed.(NCSMASK ALIM)" \ help ncsmask_alim \ label "Search limits in a" \ widget NCSMASK_ALIM_1 \ widget NCSMASK_ALIM_2 \ label " b" \ widget NCSMASK_BLIM_1 \ widget NCSMASK_BLIM_2 \ label " c" \ widget NCSMASK_CLIM_1 \ widget NCSMASK_CLIM_2 \ #--------------------------------------------------------------Solvent mask OpenFolder 5 DM_SOLVENT closed 1 hide CreateLine line \ message "Update solvent mask after a few cycles? (SOLMASK UPDATE)" \ help solmask \ widget IF_SOLMASK_UPDATE \ -toggleon \ label "Update solvent mask after" \ widget SOLMASK_UPDATE_NCYC \ label cycles CreateLine line \ label "Set mask extent if different from solvent content above" -italic CreateLine line \ message "Fraction solvent + fraction protein <= 1.0 (SOLMASK)" \ help solmask \ label "Fraction of cell: solvent" \ widget SOLMASK_FRAC_SOLV \ label " protein:" \ widget SOLMASK_FRAC_PROT CreateLine line \ message "Use Wang" \ help solmask \ widget IF_SOLMASK_WANG \ -toggleon \ label "Use Wang with radius" \ message "Default enter no radius and program will derive value" \ widget WANG_RADIUS \ label "and weighting scheme" \ widget WANG_MODE #======================================================================== OpenFolder 6 closed CreateLine line \ message "Choose the mode(s) of density modification (MODE)" \ help mode \ label "Additional density modification modes: " \ widget DM_MULTI \ label "Multi resolution" \ widget DM_SKELETON \ label "Skeleton" \ widget DM_SAYRE \ label "Sayre" CreateLine line \ message "Apply resolution limits (RESOlution)" \ help resolution \ widget EXCLUDE_RESOLUTION \ -toggleon \ message "Minimum resolution (RESOlution)" \ label "Resolution range from minimum" \ widget EXCLUDE_RESOLUTION_MIN \ message "Maximum resolution (RESOlution)" \ label " to " \ widget EXCLUDE_RESOLUTION_MAX CreateLine line \ message "Set mean density for solvent and protein regions(SOLC MEAN)" \ label "Mean density of solvent" \ help solc \ widget SOLC_MEAN_SOLVVAL \ label "and protein" \ widget SOLC_MEAN_PROTVAL CreateLine line \ message "Phase combination number of sets (COMBINE SETS )" \ help combine_sets \ label "Phase combination number of sets" \ widget DM_PHASE_COMB_NSETS CreateLine line \ message "Weight given to restored missing reflections (RESTORE )" \ help combine_restore \ label "Weight assigned to restored reflections" \ widget DM_RESTORE_WT CreateLine line \ message "REALFREE subkeywords SOLV and PROT " \ help realfree \ widget DM_REALFREE_SUB \ label "Input coords and radii for REALFREE spherical patches (optional)" \ toggle_display IF_DM_REALFREE open 1 CreateLine line \ message "X-coordinate (Angstrom)" \ help realfree \ label "Solvent patch: X" \ widget DM_SX \ message "Y-coordinate (Angstrom)" \ label "Y" \ widget DM_SY \ message "Z-coordinate (Angstrom)" \ label "Z" \ widget DM_SZ \ message "Patch radius (Angstrom)" \ label "radius" \ widget DM_SR \ toggle_display DM_REALFREE_SUB open 1 CreateLine line \ message "X-coordinate (Angstrom)" \ help realfree \ label "Protein patch: X" \ widget DM_PX \ message "Y-coordinate (Angstrom)" \ label "Y" \ widget DM_PY \ message "Z-coordinate (Angstrom)" \ label "Z" \ widget DM_PZ \ message "Patch radius (Angstrom)" \ label "radius" \ widget DM_PR \ toggle_display DM_REALFREE_SUB open 1 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 CreateLine line \ label "Skeletonisation options:" -italic CreateLine line \ message "Skeletonisation applied every n cycles (SKEL EVERY)" \ help skel \ label "Apply skeletonisation every " \ widget DM_SKEL_CYCLES \ label "cycles" CreateLine line \ message "Length of skeleton in A/residue between density peaks (SKEL LENGTH joinlen)" \ help skel \ label "Length per residue of connected skeleton" \ widget DM_SKEL_JOINLEN \ message "Length of skeleton in A/residue to apply to trailing ends (SKEL LENGTH endlen)" \ label "and for side chains" \ widget DM_SKEL_ENDLEN CreateLine line \ message "temperature factor applied to sharpened map before skeletonisation (SKEL BFAC)" \ help skel \ label "Map smoothing temperature factor" \ widget DM_SKEL_BFAC }