# # 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 $Id$ # ====================================================================== # watertidy.tcl -- # # CCP4Interface # # ======================================================================= # procedure which is run automatically before drawing the interface # used to set up variables, menus etc #--------------------------------------------------------------------- proc watertidy_setup { typedefVar arrayname } { #--------------------------------------------------------------------- upvar #0 $arrayname array upvar #0 $typedefVar typedef DefineMenu _watertidy_symm_mode [ list "list of operators" \ "spacegroup" ] \ [ list LIST \ SPGRP ] return 1 } #--------------------------------------------------------------------- proc watertidy_run { arrayname } { #--------------------------------------------------------------------- upvar #0 $arrayname array if { [regexp SPGRP [GetValue $arrayname SYMM_MODE] ] && ![IfSet $array(SPACE_GROUP)] } { WarningMessage "You must enter a space group before running the program" return 0 } if {![IfSet $array(WATIN_ID)] } { WarningMessage "You must enter a water chain id before running the program" return 0 } return 1 } # procedure for adding to the list of symmetry operations #--------------------------------------------------------------------- proc watertidy_add_symop { arrayname counter } { #--------------------------------------------------------------------- CreateLine line \ message "Add a symmetry operator in format eg X+1/2, Y+1/2, -Z (SYMM keyword)" \ help symm \ label "Operator" \ label $counter \ widget SYMOP -width 30 } #--------------------------------------------------------------------- proc watertidy_radius { arrayname counter } { #--------------------------------------------------------------------- CreateLine line \ help radii \ message "Enter search radii for atom types (RADII)" \ label "Atom type" \ widget ATOMTYPE \ label "search radius" \ widget ATOMRADIUS } # procedure for adding chains to the list #--------------------------------------------------------------------- proc watertidy_add_chain { arrayname counter } { #--------------------------------------------------------------------- CreateLine line \ help chnid \ message "Host chain identifier" \ label "Protein chain id" \ widget CHAIN_ID -width 5 -oblig \ label "residue range" \ widget CHAIN_RES_1 \ label to \ widget CHAIN_RES_2 # message "Output water chain id as it will appear in output file" \ # label "chain id for nearby waters" \ # widget WATOUT_ID -width 5 -oblig } # procedure to draw task window #--------------------------------------------------------------------- proc watertidy_task_window { arrayname } { #--------------------------------------------------------------------- upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "Rationalise waters at end of refinement" "Watertidy" \ [ list "Symmetry for Distang and Watertidy" \ "Search radii for atom types (Distang)" \ "Chain details (pdb file input/output)" \ "Other parameters" ] ] == 0 } return # Set the name of the CCP4 program help file to use SetProgramHelpFile "watertidy" #=PROTOCOL============================================================== OpenFolder protocol CreateTitleLine line TITLE CreateLine line \ help shell \ message "Default mode is to run three cycles to find shells 1 to 3" \ label "Run multiple cycles to find water in shells" \ widget FIRST_SHELL \ label to \ widget LAST_SHELL #=FILES================================================================ OpenFolder file CreateInputFileLine line \ "Enter name of input pdb file" \ "PDB in" \ XYZIN DIR_XYZIN \ -setfileparam space_group_name SPACE_GROUP \ -fileout XYZOUT DIR_XYZOUT _watertidy \ -command "WaterTidyReadPdb $arrayname" CreateOutputFileLine line \ "Enter output pdb file name" \ "PDB out" \ XYZOUT DIR_XYZOUT #--------------------------------------------------SYMMETRY folder OpenFolder 1 CreateLine line \ message "Select method for entering symmetry operations" \ label "Use" \ widget SYMM_MODE \ label "to define symmetry operations" CreateLine line \ help symmetry \ message "Enter spacegroup name or number (SPACEGROUP)" \ label "Spacegroup:" \ widget SPACE_GROUP -oblig \ toggle_display SYMM_MODE open [ list SPGRP ] OpenSubFrame frame \ -toggle_display SYMM_MODE open [ list LIST ] CreateLine line \ label "List of individual symmetry operators:" -italic CreateExtendingFrame NSYMM watertidy_add_symop \ "Add to the list of individual symmetry operations" \ "Add symmetry operation" \ [ list SYMOP ] CloseSubFrame #--------------------------------------------------SEARCH RADII # This folder sets the radii for the contacts routine OpenFolder 2 closed CreateExtendingFrame N_ATOM_RADII watertidy_radius \ "Set atomic radius" \ "Add new atom type" \ [list ATOMTYPE ATOMRADIUS ] #--------------------------------------------------CHAIN IDS # This folder sets the chain ids OpenFolder 3 CreateExtendingFrame NHOST_CHAIN watertidy_add_chain \ "Add to the list of host chains" \ "Add host chain" \ [ list CHAIN_ID CHAIN_RES_1 CHAIN_RES_2 WATOUT_ID ] CreateLine line \ help watid \ message "Chain identifier for unassigned waters" \ label "Water chain id as it appears in the input file: " \ widget WATIN_ID -oblig #--------------------------------------------------OTHER PARAMTERS # This folder sets the Keys ACCEPT, HBOND and OCCW. OpenFolder 4 closed CreateLine line \ help accept \ message "Specify extra acceptors: single character atom types" \ label "Specify extra acceptors: " \ widget ACCEPTORS \ label "(default O N )" CreateLine line \ help hbond \ message "Maximum number of waters bonded to one atom" \ label "Maximum number of H-bonds per atom: " \ widget HBOND \ label "(4)" CreateLine line \ help occw \ message "Occupancy for secondary sites. If 0.0 not output." \ label "Occupancy for secondary sites: " \ widget OCCW \ label "(0.01)" } #------------------------------------------------------------------- proc WaterTidyReadPdb { arrayname } { #------------------------------------------------------------------- upvar #0 $arrayname array source [SearchPath TOP utils pdb_utils.tcl] if { [PdbGetChains [GetFullFileName0 $arrayname XYZIN] chains chain_res -nowat] \ && [llength $chains] > 0 } { set increment [expr [llength $chains] - $array(NHOST_CHAIN) ] update_extendingframe watertidy_add_chain 0 $arrayname NHOST_CHAIN \ $array(NHOST_CHAIN) $increment 1 for { set n 1 } { $n <= $array(NHOST_CHAIN) } { incr n } { set array(CHAIN_ID,$n) [lindex $chains [expr $n -1] ] set array(CHAIN_RES_1,$n) [lindex [lindex $chain_res [expr $n -1] ] 0] set array(CHAIN_RES_2,$n) [lindex [lindex $chain_res [expr $n -1] ] 1] set_field_colour $arrayname CHAIN_ID,$n 1 } } }