# ------------------------------------------------------------------- # # Copyright (C) 2005-2011 by Global Phasing Limited # # This code is distributed under the terms and conditions of the CCP4 # Program Suite Licence Agreement as a CCP4 Application. A copy of # the CCP4 licence can be obtained by writing to the CCP4 Secretary, # Daresbury Laboratory, Warrington WA4 4AD, UK. # # Authors: (2005-2011) Clemens Vonrhein # # ------------------------------------------------------------------- #CCP4i_cvs_Id $Id$ set typedef(_RFL_file) { file RFL ".mtz,.sca,.hkl" "reflection data" "" "" } set typedef(_HATOM_file) { file HATOM ".hatom" "hatom file" "" "" } #-------------------------------------------------------------------- # This is called by CCP4i to check whether the necessary prerequisites # exist on the system for this interface to run # Returns 1 if prereqs exist, zero otherwise proc autoSHARP_prereq { } { if { [GetEnvPath BDG_home 0] == "" && [GetEnvPath SHARP_home 0] == "" } { # No environment variable BDG_home/SHARP_home return 0 } else { if { [GetEnvPath SHARP_home 0] != "" } { set SHARP_home [GetEnvPath SHARP_home] if { ! [file exists [FileJoin $SHARP_home bin sharp detect.sh] ] } { return 0 } } else { set BDG_home [GetEnvPath BDG_home] if { ! [file exists [FileJoin $BDG_home bin sharp detect.sh] ] } { return 0 } } } return 1 } # procedure which is run automatically before drawing the interface # used to set up variables, menus etc proc autoSHARP_setup { typedefVar arrayname } { upvar #0 $typedefVar typedef upvar #0 $arrayname array set typedef(_RFL_file) { file RFL ".mtz,*.sca,*.hkl" "reflection data" "" "" } lappend typedef(file_types) _RFL_file set typedef(_HATOM_file) { file HATOM ".hatom" "hatom file" "" "" } lappend typedef(file_types) _HATOM_file # Define the 'autosharp_type' menu DefineMenu _autosharp_type [list "SAD/MAD" "SIR(AS)/MIR(AS)" ] \ [ list MAD MIR ] # Define the 'autosharp_data_format' menu DefineMenu _autosharp_data_format [list "MTZ" "SCALEPACK (merged)" "SCALEPACK (unmerged)" "SHELX HKL4" "MTZ (relative scaled)"] \ [ list MTZ SCAM SCAU HKL MTZS] DefineMenu _autosharp_spgr [list None P1 P2 P112 P21 I21 P1121 A2 C2 C21 P222 P2221 P21212 \ P21212a P21221 P22121 P212121 C2221 C2221a C222 C222a F222 F222a I222 I222a \ I212121 P4 P41 P42 P43 I4 I41 P422 P4212 P4122 P41212 P4222 \ P42212 P42212a P4322 P43212 I422 I4122 P3 P31 P32 H3 P312 P321 \ P3112 P3121 P3212 P3221 H32 P6 P61 P65 P62 P64 P63 P622 P6122 \ P6522 P6222 P6422 P6322 P23 F23 I23 I23a P213 I213 P432 P4232 \ F432F4132 I432 P4332 P4132 I4132] \ [list None P1 P2 P112 P21 I21 P1121 A2 C2 C21 P222 P2221 P21212 \ P21212a P21221 P22121 P212121 C2221 C2221a C222 C222a F222 F222a I222 I222a \ I212121 P4 P41 P42 P43 I4 I41 P422 P4212 P4122 P41212 P4222 \ P42212 P42212a P4322 P43212 I422 I4122 P3 P31 P32 H3 P312 P321 \ P3112 P3121 P3212 P3221 H32 P6 P61 P65 P62 P64 P63 P622 P6122 \ P6522 P6222 P6422 P6322 P23 F23 I23 I23a P213 I213 P432 P4232 \ F432F4132 I432 P4332 P4132 I4132] DefineMenu _autosharp_rate [list "1 - fast" "2 - ......" "3 - ........" "4 - .........." "5 - accurate"] \ [list 1 2 3 4 5] DefineMenu _autosharp_viewer [list "none" "O" "XtalView" "Coot"] [list "NONE" "O" "Xfit" "Coot"] DefineMenu _autosharp_entrypoint3_path [list "(1) Data analysis" "(2) + Heavy atom detection" "(3) + Heavy atom refinement & phasing" "(4) + Density modification" "(5) + Automatic model building"] \ [list 43 53 63 73 83] DefineMenu _autosharp_detectpgm [list "SHELXD" "RANTAN"] \ [list shelx rantan] return 1 } #-------------------------------------------------------------------- # this procedure is run when user clicks the 'Run' button # used to check user input and where necessary convert parameters # to form required by the program run script # proc autoSHARP_run1 { arrayname } { # upvar #0 $arrayname array # set bdg_home [ GetEnvPath BDG_home ] # if { ![IfSet $bdg_home] } { # WarningMessage "Environmental variable BDG_home is not set." # return 0 # } # if ( ![file isdirectory $bdg_home] } { # WarningMessage "Environmental variable BDG_home doesn't point to a directory." # return 0 # } # set licence [FileJoin $BDG_home .licence ] # if ( ![file exists $licence] } { # WarningMessage "File $licence doesn't exist." # return 0 # } # if ( ![file isfile $licence] } { # WarningMessage "$licence is not a file." # return 0 # } # if ( ![file readable $licence] } { # WarningMessage "File $licence is not readable." # return 0 # } # return 1 #} proc autoSHARP_run { arrayname } { upvar #0 $arrayname array set sharp_home [ GetEnvPath SHARP_home ] if { [IfSet $sharp_home] } { set env(BDG_home) [GetEnvPath SHARP_home] set home_name "SHARP_home" } else { set home_name "BDG_home" } set bdg_home [ GetEnvPath BDG_home ] if { ![IfSet $bdg_home] } { WarningMessage "Environmental variable $home_name is not set." return 0 } if { ![file isdirectory $bdg_home] } { WarningMessage [join [list "Environmental variable $home_name (" $bdg_home ") doesn't point to a directory." ] ] return 0 } set licence [FileJoin $bdg_home .licence ] if { ![file exists $licence] } { WarningMessage "File $licence doesn't exist." return 0 } if { ![file isfile $licence] } { WarningMessage "$licence is not a file." return 0 } if { ![file readable $licence] } { WarningMessage "File $licence is not readable." return 0 } return 1 } #--------------------------------------------------------------------- proc autoSHARP_task_window { arrayname } { # procedure to draw task window upvar #0 $arrayname array if { [ CreateTaskWindow $arrayname "autoSHARP: automated structure solution with SHARP" "autoSHARP" \ [ list "General parameters" "Asymmetric Unit" "Dataset parameters" ] ] == 0 } { return } set bdg_help "[file join [GetEnvPath BDG_home] docs sharp manual autoSHARP2.html]" SetProgramHelpFile $bdg_help # protocol OpenFolder protocol CreateLine line \ label "NOTE This task uses the SHARP/autoSHARP programs which are not distributed with CCP4 - see: www.globalphasing.com" -italics CreateLine line \ label "NOTE The job title should be given in a format suitable to create directories from - so no space, #, / etc" -italics CreateTitleLine line TITLE CreateLine line_type \ message "Description of autoSHARP run" \ help "titl" \ label "Description" \ widget autoSHARP_titl CreateLine line_type \ message "Description of autoSHARP experiment" \ help "prepare" \ label "Run a" \ widget autoSHARP_type \ label "experiment" # with " \ message "Number of wavelengths (SAD/MAD) or derivatives (SIR/MIR)" \ help "prepare" \ widget autoSHARP_nset \ label "wavelength(s)/derivative(s)" CreateLine line_format \ message "format of input files" \ help "prepare" \ label "Input file(s) is/are in" \ widget autoSHARP_data_format \ label "format with spacegroup " \ message "override spacegroup in files (if present) or leave at None" \ help "symm" \ widget autoSHARP_spgr CreateLine line_rate \ message "Decide if run should be fast, accurate or a compromise of these" \ help "prepare" \ label "Speed vs. accurate setting of" \ widget autoSHARP_rate CreateLine line_steps \ message "Which (successive) steps to perform" \ help "what" \ label "Run up to (and including)" \ widget autoSHARP_EntryPoint3_Path \ message "Which program to use for heavy atom detection" \ help "hatm" \ label "using" \ widget autoSHARP_DetectPgm \ label "for HA detection" CreateLine line_viewer \ message "Decide which viewer will be used for looking at maps/models" \ help "viewer" \ label "Prepare results (maps/models) for viewing with " \ widget autoSHARP_viewer # general OpenFolder 1 CreateLine line \ message "Apply resolution limits" \ help "reso" \ widget autoSHARP_res \ -toggleon \ message "Low resolution limit" \ label "Resolution range from" \ widget autoSHARP_resl \ message "High resolution limit" \ label " to " \ widget autoSHARP_resh # molecular weight OpenFolder 2 CreateInputFileLine line_pir \ "PIR formatted sequence file (monomer) - this is the preferred option" \ "Sequence (preferred)" \ autoSHARP_pirf DIR_autoSHARP_pirf \ -notoblig CreateLine line_nres \ label " OR : no. of residues" \ message "No. of residues in monomer - please use sequence file instead" \ help "molw" \ widget autoSHARP_nres CreateLine line_mw \ message "Molecular weight (Dalton) of monomer - please use sequence file instead" \ help "molw" \ label " OR : molecular weight" \ widget autoSHARP_molw CreateLine line \ message "Type of heavy atom" \ help "hatm" \ label "Atom type" \ widget autoSHARP_hatm,0 \ message "Number of expected sites (per monomer)" \ help "hatm" \ label "No. of sites" \ widget autoSHARP_nsit,0 \ toggle_display autoSHARP_type open [list MAD] CreateInputFileLine line \ "File with known sites" \ "hatom file" \ autoSHARP_sitf_mad DIR_autoSHARP_sitf_mad \ -notoblig \ -toggle_display autoSHARP_type open [list MAD] # datasets OpenFolder 3 CreateToggleFrame autoSHARP_nset autosharp_dataset_def \ "Definition of various datasets" "Dataset no." \ "Add another dataset" \ [list autoSHARP_iden autoSHARP_wave autoSHARP_hatm autoSHARP_nsit \ autoSHARP_fone autoSHARP_ftwo autoSHARP_fmid \ autoSHARP_smid autoSHARP_dano autoSHARP_sano autoSHARP_isym \ autoSHARP_dtyp autoSHARP_data DIR_autoSHARP_data \ autoSHARP_LABIN autoSHARP_data_mtz DIR_autoSHARP_data_mtz \ autoSHARP_data_sca DIR_autoSHARP_data_sca autoSHARP_sitf DIR_autoSHARP_sitf] } #--------------------------------------------------------------------- proc autosharp_dataset_def { arrayname counter } { # procedure to draw dataset form upvar #0 $arrayname array set autoSHARP_type [GetValue $arrayname autoSHARP_type] set autoSHARP_data_format [GetValue $arrayname autoSHARP_data_format] CreateLine line \ message "Short string as identifier" \ help "iden" \ label "Identifier" \ widget autoSHARP_iden \ message "Wavelength (in Angstroem)" \ help "wave" \ label "Wavelength" \ widget autoSHARP_wave \ message "f' value for given heavy atom" \ help "wave" \ label " f' " \ widget autoSHARP_fone \ message "f'' value for given heavy atom" \ label " f'' " \ help "wave" \ widget autoSHARP_ftwo \ toggle_display autoSHARP_type open [list MAD] if { $counter > 1 } { CreateLine line \ message "Short string as identifier" \ label "Identifier" \ widget autoSHARP_iden \ message "Wavelength (in Angstroem)" \ help "wave" \ label "Wavelength" \ widget autoSHARP_wave \ message "f' value for given heavy atom" \ help "wave" \ label " f' " \ widget autoSHARP_fone \ message "f'' value for given heavy atom" \ help "wave" \ label " f'' " \ widget autoSHARP_ftwo \ message "Type of heavy atom" \ help "hatm" \ label "Atom type" \ widget autoSHARP_hatm \ message "Number of expected sites (per monomer)" \ help "hatm" \ label "No. of sites" \ widget autoSHARP_nsit \ toggle_display autoSHARP_type open [list MIR] } else { CreateLine line \ message "Short string as identifier (for native)" \ help "iden" \ label "Identifier" \ widget autoSHARP_iden \ toggle_display autoSHARP_type open [list MIR] } CreateInputFileLine line \ "Input MTZ file" \ "Datafile" \ autoSHARP_data_mtz DIR_autoSHARP_data_mtz \ -setfileparam space_group_name SPACE_GROUP \ -setfileparam cell_1 CELL_1 \ -setfileparam cell_2 CELL_2 \ -setfileparam cell_3 CELL_3 \ -setfileparam cell_4 CELL_4 \ -setfileparam cell_5 CELL_5 \ -setfileparam cell_6 CELL_6 \ -toggle_display autoSHARP_data_format open [list MTZ MTZS] CreateLabinLine line \ "Observed amplitude (F) and sigma (SIGF)" \ autoSHARP_data_mtz,$counter FMID autoSHARP_fmid [list F FP autoSHARP_fmid] \ -sigma SMID autoSHARP_smid [list SIGF SIGFP autoSHARP_smid] \ -toggle_display autoSHARP_data_format open [list MTZ MTZS] if { $autoSHARP_type == "MAD" || $counter > 1 } { CreateLabinLine line \ "Anomalous difference (autoSHARP_dano) and sigma (SIGautoSHARP_dano)" \ autoSHARP_data_mtz,$counter DANO autoSHARP_dano [list autoSHARP_dano] \ -sigma SANO autoSHARP_sano [list SIGautoSHARP_dano autoSHARP_sano] \ -toggle_display autoSHARP_data_format open [list MTZ MTZS] CreateLabinLine line \ "autoSHARP_isym column" \ autoSHARP_data_mtz,$counter ISYM autoSHARP_isym [list autoSHARP_isym] \ -toggle_display autoSHARP_data_format open [list MTZ MTZS] } CreateInputFileLine line \ "Input reflection file" \ "Datafile" \ autoSHARP_data_sca DIR_autoSHARP_data_sca \ -toggle_display autoSHARP_data_format hide [list MTZ MTZS] CreateLine line \ message "Enter cell lengths(Angstrom) and angles(degs) (CELL)" \ help "cell" \ label "Cell dimensions " \ widget autoSHARP_cel1 -oblig \ widget autoSHARP_cel2 -oblig \ widget autoSHARP_cel3 -oblig \ widget autoSHARP_cel4 -oblig \ widget autoSHARP_cel5 -oblig \ widget autoSHARP_cel6 -oblig \ toggle_display autoSHARP_data_format open [list SCAU] if { $autoSHARP_type == "MIR" && $counter > 1 } { CreateInputFileLine line \ "File with known sites" \ "hatom file" \ autoSHARP_sitf DIR_autoSHARP_sitf \ -notoblig } return 1 }