# # 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 $Id$ # ====================================================================== # shelx.tcl -- # # Run shelx program for direct methods or patterson search # # CCP4Interface # # ======================================================================= #------------------------------------------------------------------------------ proc shelx_prereq { } { #------------------------------------------------------------------------------ global configure if { ![file exists [FindExecutable "$configure(SHELX)"]] } { return 0 } return 1 } #------------------------------------------------------------------------------ proc shelx_setup { typedefVar arrayname } { #------------------------------------------------------------------------------ upvar #0 $typedefVar typedef set typedef(_shelx_mode) { menu { "Patterson search" "direct methods" } { PATTERSON DIRECT } } set typedef(_shelx_input_format) { menu { "MTZ file" "Shelx hkl file" } { MTZ SHELX } } set typedef(_shelx_hklf) { menu { "normalised amplitudes" intensities } { 3 4 } } set typedef(_shelx_lattice) { menu { primitive "body centred" "face centred" \ "A-face centred" "B-face centred" "C-face centred" } { -1 -2 -4 -5 -6 -7 } } set typedef(_shelx_data_type) { menu { isomorphous anomalous } } return 1 } #------------------------------------------------------------------------------ proc shelx_run { arrayname } { #------------------------------------------------------------------------------ upvar #0 $arrayname array global configure if { [ regexp MTZ [GetValue $arrayname INPUT_FORMAT ]] } { set array(INPUT_FILES) MTZIN set array(LABIN) "FP SIGFP" if { [regexp isomorphous [GetValue $arrayname DATA_TYPE] ] } { append array(LABIN) " FPH SIGFPH" } else { append array(LABIN) " DP SIGDP" } } else { set array(INPUT_FILES) HKLIN } set array(SFAC_LIST) "N $array(HEAVY_TYPE)" set array(UNIT_LIST) "200 $array(NHEAVY)" # for { set n 1 } { $n <= $array(N_SFAC) } { incr n } { # append array(SFAC_LIST) $array(SFAC,$n) " " # append array(UNIT_LIST) $array(UNIT,$n) " " # } if { [ElementExists configure SHELX] && $configure(SHELX) != "" } { set array(SHLEX_PROGRAM) $configure(SHELX) } return 1 } #----------------------------------------------------------------------- proc ShelxSfac { arrayname counter } { #----------------------------------------------------------------------- CreateLine line \ label "Element" \ widget SFAC \ label "Number of atoms" \ widget UNIT } #----------------------------------------------------------------------- proc ShelxVect { arrayname counter } { #----------------------------------------------------------------------- CreateLine line \ label "Vector x" \ widget VECT_X \ label " y" \ widget VECT_Y \ label " z" \ widget VECT_Z } #---------------------------------------------------------------------- proc shelx_set_lattice { arrayname } { #---------------------------------------------------------------------- upvar #0 $arrayname array SetValue $arrayname LATTICE \ [GetLatticeFromSpaceGp $array(SPACE_GROUP) -shelx ] } #----------------------------------------------------------------------- proc shelx_task_window { arrayname } { #----------------------------------------------------------------------- upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "Shelx - Heavy Atom Search" "Shelx" \ [ list "Cell Parameters" \ "Exclude Reflections" \ "Shelx Patterson Search Parameters" \ "Shelx Direct Methods Parameters" ] ] == 0 } return SetProgramHelpFile "shelx" #=PROTOCOL============================================================== OpenFolder protocol CreateLine line \ label "NOTE This task uses the Shelx program which is not distributed with CCP4 - click Help for details" -italics CreateTitleLine line TITLE CreateLine line \ label "Try to find heavy atoms by" \ widget SHELX_MODE CreateLine line \ label "Input format is" \ widget INPUT_FORMAT \ label "using" \ widget DATA_TYPE \ label data \ toggle_display INPUT_FORMAT open MTZ CreateLine line \ label "Input format is" \ widget INPUT_FORMAT \ label "data is" \ widget SHELX_HKLF \ toggle_display INPUT_FORMAT open SHELX #=FILES================================================================ OpenFolder file OpenSubFrame frame -toggle_display INPUT_FORMAT open SHELX CreateInputFileLine line \ "Enter input HKL file name (HKLIN)" \ "HKL in" \ HKLIN DIR_HKLIN CreateLine line \ label "Optionally extract cell parameters from MTZ file.." -italic CloseSubFrame CreateInputFileLine line \ "Enter input MTZ file name (MTZIN)" \ "MTZ in" \ MTZIN DIR_MTZIN \ -setfileparam resolution_min EXCLUDE_RESOLUTION_MIN \ -setfileparam resolution_max EXCLUDE_RESOLUTION_MAX \ -setfileparam cell CELL \ -setfileparam space_group_name SPACE_GROUP \ -command "shelx_set_lattice $arrayname" OpenSubFrame frame -toggle_display INPUT_FORMAT open MTZ CreateLabinLine line \ "Protein experimental amplitude (FP) and optional sigma (SIGFP)" \ MTZIN FP FP [list F FP] \ -sigma Sigma SIGFP {} CreateLabinLine line \ "Derivative experimental amplitude (FPH) and optional sigma (SIGFPH)" \ MTZIN FPH FPH [list FPH] \ -sigma SigmaPH SIGFPH {} \ -toggle_display DATA_TYPE open isomorphous CreateLabinLine line \ "Anomalous data (DP SIGDP)" \ MTZIN DP DP [list DP] \ -sigma SIGDP SIGDP [list SIGDP] \ -toggle_display DATA_TYPE open anomalous CloseSubFrame #-------------------------------------------------------------------- OpenFolder 1 SetProgramHelpFile shelx CreateLine line \ message "Space group (default as in MTZ file) (SYMMETRY)" \ label "Space group" \ help symmetry \ widget SPACE_GROUP -oblig -command "shelx_set_lattice $arrayname" \ label "and lattice type" \ help lattice \ widget LATTICE -oblig \ label " Wavelength" \ widget CELL_LAMBDA -oblig CreateLine line \ message "Cell dimensions (default from MTZ file) (CELL)" \ help cell \ label "Set cell a" \ widget CELL_1 -width 8 -oblig \ label "b" \ widget CELL_2 -width 8 -oblig \ label "c" \ widget CELL_3 -width 8 -oblig \ label "alpha" \ widget CELL_4 -width 8 -oblig \ label "beta" \ widget CELL_5 -width 8 -oblig \ label "gamma" \ widget CELL_6 -width 8 -oblig CreateLine line \ message "Estimates standard deviations on cell dimensions (ZERR)" \ label "Cell ESDs a" \ widget CELL_ERR_1 -width 8 -oblig \ label "b" \ widget CELL_ERR_2 -width 8 -oblig \ label "c" \ widget CELL_ERR_3 -width 8 -oblig \ label "alpha" \ widget CELL_ERR_4 -width 8 -oblig \ label "beta" \ widget CELL_ERR_5 -width 8 -oblig \ label "gamma" \ widget CELL_ERR_6 -width 8 -oblig CreateLine line \ message "Enter number of heavy atoms to search for" \ label "Search for" \ widget NHEAVY \ label "atoms of" \ widget HEAVY_TYPE # CreateLine line \ # message "Number of copies of formula units (Z)" \ # label "Number of copies of formula defined below" \ # widget CELL_Z # CreateExtendingFrame N_SFAC ShelxSfac \ # "Define composition of one molecule" \ # "Add Element" \ # [list SFAC UNIT ] #------------------------------------------------------------------------------- OpenFolder 3 SHELX_MODE open PATTERSON hide CreateLine line \ label Try \ widget TRY_NVECTORS \ label "superposition vectors" CreateLine line \ label "Enter 'known' vectors:" -italic CreateExtendingFrame INPUT_NVECT ShelxVect \ "Enter 'known' vectors" \ "Add Vector" \ [list VECT_X VECT_Y VECT_Z ] #----------------------------------------------------------------------------------- OpenFolder 4 SHELX_MODE open DIRECT hide CreateLine line \ label Try \ message "Override default TREF np - set to 5000 for difficult structures" \ widget TREF_NP \ label "direct methods attempts using" \ message "Override default TREF nE" \ widget TREF_NE \ label reflections in the full tangent formula" CreateLine line \ message "Fudge factor allow for exptl error & avoid 'uranium' solution (TREF kapscal)" \ label "Multiple products of Es in triplet phase relation by" \ widget TREF_KAPSCAL #----------------------------------------------------------------------------------- OpenFolder 2 INPUT_FORMAT closed MTZ hide CreateLine line \ message "Exclude reflections below and/or above resolution limit in \ Angstrom (RESOLUTION)" \ help resolution \ widget EXCLUDE_RESOLUTION \ -toggleon \ label "Resolution less than" \ widget EXCLUDE_RESOLUTION_MIN \ label "Angstrom or greater than" \ widget EXCLUDE_RESOLUTION_MAX \ label "Angstrom" CreateLine line \ message "Exclude reflections in set selected for FreeR \ calculation (FREERFLAG&FREE)" \ help include_freer \ widget EXCLUDE_FREER \ label "FreeR label" \ widget EXCLUDE_FREER_LABEL \ label "of value " \ widget EXCLUDE_FREER_VALUE CreateLineTemplate "EXCLUDE" {0.0 0.6 0.8} CreateLine line \ message "Exclude FPs which are small compared to sigma FP (EXCLUDE SIGP)" \ help exclude_sigp \ widget EXCLUDE_SIGP \ -toggleon \ label "FP less than n * sigmaF where n is " \ widget EXCLUDE_SIGP_FACTOR \ format template "EXCLUDE" CreateLine line \ message "Exclude FPHs which are small compared to sigma FPH(EXCLUDE SIGH)" \ help exclude_sigp \ widget EXCLUDE_SIGH \ -toggleon \ label "FPH less than n * sigmaFH where n is " \ widget EXCLUDE_SIGH_FACTOR \ format template "EXCLUDE" CreateLine line \ message "Exclude refs with small absolute FP values(EXCLUDE FPMAX)" \ help exclude_fpmax \ widget EXCLUDE_FPMAX \ -toggleon \ label "F absolute value less than " \ widget EXCLUDE_FPMAX_MAX \ format template "EXCLUDE" CreateLine line \ message "Exclude refs with large diff between FP and FPH (EXCLUDE DIFF)" \ help exclude_diff \ widget EXCLUDE_DIFF \ -toggleon \ label "Difference between F1 and F2 greater than" \ widget EXCLUDE_DIFF_LIMIT \ format template "EXCLUDE" }