#
# 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 $Id$
#=========================================================================
#
# refmac.script
#
#=========================================================================
# Source pdb_utils for harvest handling & move to project directory
# if we are going to dump harvest file to current directory
source [SearchPath TOP utils pdb_utils.tcl ]
if { [StringSame $HARVEST_MODE CURRENTDIR ] } { ChangeDirectory [GetDefaultDirPath] }
# Source the utils/maps_utils.tcl script for map drawing
if { $IF_MAPOUT } {
source [SearchPath TOP utils map_utils.tcl] }
#---------------------------------------------------------------------
# Prosmart script
#---------------------------------------------------------------------
if { $IFPROSMART && ![regexp INPUT $PROSMART_MODE ] } {
# set output directory
set prosmart_output_dir [ FileJoin [GetDefaultDirPath] $job_params(JOB_ID)_prosmart ]
AddOutputDir $prosmart_output_dir
set cmd "[BinPath prosmart] -p1 \"$XYZIN\" -o \"$prosmart_output_dir\""
if { $IFEXTREST_USEMAIN } {
append cmd " -main"
} else {
append cmd " -side"
}
if { $USE_PROSMART_KEYFILE } {
append cmd " -f $PROSMART_KEYFILE"
}
if [regexp DNARNA $PROSMART_MODE ] {
append cmd " -dna_rna"
}
if { [regexp EXTERNAL $PROSMART_MODE ] || [regexp DNARNA $PROSMART_MODE ] } {
# using prosmart for external restraints to reference structure
append cmd " -p2 \"$EXT_XYZIN\""
set restraint_file [ FileJoin $prosmart_output_dir Output_Files \
Restraints [FileRootName $XYZIN].txt ]
WriteToLog "\n *** Starting Prosmart to determine restraints to external structure *** \n Using command: $cmd \n Writing results to directory $prosmart_output_dir \n"
} elseif [regexp HBOND $PROSMART_MODE ] {
# using prosmart for h-bond restraints
append cmd " -h"
if { !$PROSMART_HBOND } {
if { $PROSMART_HBONDHELIX3 } {
append cmd " -3_10"
}
if { $PROSMART_HBONDHELIX4 } {
append cmd " -alpha"
}
if { $PROSMART_HBONDHELIX5 } {
append cmd " -pi"
}
if { $PROSMART_HBONDSHEET } {
append cmd " -h_sheet"
}
}
if { !$PROSMART_HBOND && $PROSMART_HBONDSHEET && !$PROSMART_HBONDHELIX3 && !$PROSMART_HBONDHELIX4 && !$PROSMART_HBONDHELIX5 } {
set restraint_file [ FileJoin $prosmart_output_dir Output_Files \
Restraints LIB_[FileRootName $XYZIN].txt ]
} else {
set restraint_file [ FileJoin $prosmart_output_dir Output_Files \
Restraints [FileRootName $XYZIN].txt ]
}
WriteToLog "\n *** Starting Prosmart to determine h-bond restraints *** \n Using command: $cmd \n Writing results to directory $prosmart_output_dir \n"
} else {
# using prosmart for secondary structure restraints
if { $PROSMART_HELIX } {
append cmd " -helix"
}
if { $PROSMART_STRAND } {
append cmd " -strand"
}
set restraint_file [ FileJoin $prosmart_output_dir Output_Files \
Restraints LIB_[FileRootName $XYZIN].txt ]
WriteToLog "\n *** Starting Prosmart to determine secondary structure restraints *** \n Using command: $cmd \n Writing results to directory $prosmart_output_dir \n"
}
set status [Execute $cmd "" program_status report ]
if { ![file exists $restraint_file] } {
WriteToLog "Restraint file not generated by Prosmart - check Prosmart logfile"
TerminateScript 0 -report "Prosmart failed to generate a file of restraints"
}
WriteToLog "\n *** Prosmart finished *** \n Copying file of restraints $restraint_file to $RESTRAINTFILE \n"
CopyFile $restraint_file $RESTRAINTFILE
}
#---------------------------------------------------------------------
# Libg script
#---------------------------------------------------------------------
if { $IF_LIBG } {
# set output directory
set libg_output_dir [ FileJoin [GetDefaultDirPath] $job_params(JOB_ID)_libg ]
set cmd "[BinPath libg] -o \"$LIBG_RESTRAINTFILE\" -p \"$XYZIN\""
if { $USE_LIBG_DICTFILE } {
append cmd " -d $LIBG_DICTFILE"
}
if [regexp MANULY $LIBG_MODE ] {
# using libg in user's defined mode
append cmd " -u \"$USE_LIBG_KEYFILE\""
}
#CreateComScript libg libg_script
set status [Execute $cmd "" program_status report ]
}
#---------------------------------------------------------------------
# Refmac script
#---------------------------------------------------------------------
if [regexp REVIEW $REFINE_TYPE] {
foreach param [list MAKE_CHECK MAKE_PEPTIDE MAKE_CISPEPTIDE \
MAKE_SSBRIDGE MAKE_SYMMETRY MAKE_CHAIN MAKE_NEWLIGAND MAKE_CONNECTIVITY \
MAKE_LINK MAKE_SUGAR ] {
eval set $param \$REVIEW_$param
}
set MAKE_REVIEW 1
} else {
set MAKE_REVIEW 0
# If not in REVIEW mode then set up a job-specific name
# for LIBOUT
set LIBOUT "[SetOutputFileRoot]_lib.cif"
}
if { [regexp TLS $REFINE_TYPE ] } {
set IFTLS 1
set REFINE_TYPE REST
} else {
set IFTLS 0
}
if [regexp ANIS $B_REFINEMENT_MODE] {
set REFINE_ANISO 1
} else {
set REFINE_ANISO 0
}
CreateComScript refmac5 refmac_script
#################################################################################
#------------------------------------------------------------------------------
# Run cycles of refmac (coot etc )
#------------------------------------------------------------------------------
#################################################################################
set CURRENT_PDB $XYZIN
set CURRENT_MTZ $HKLIN
set CURRENT_TLS $TLSIN
if {$EXTERNAL_NCYCLES < 1} { set EXTERNAL_NCYCLES 1 }
for { set loop 1 } { $loop <= $EXTERNAL_NCYCLES } { incr loop } {
# Set the output PDB, MTZ and TLS file variables (15/10/09: removed the old option of
# outputting a temporary file in each loop. This is no longer neccessary. RMK)
set NEW_PDB $XYZOUT
set NEW_MTZ $HKLOUT
set NEW_TLS $TLSOUT
DeleteFile $NEW_PDB
DeleteFile $NEW_MTZ
DeleteFile $NEW_TLS
#------------------------------------------------------------------------------
# run refmac
#------------------------------------------------------------------------------
set cmd "[BinPath refmac5] XYZIN \"$CURRENT_PDB\" XYZOUT \"$NEW_PDB\""
if { ![StringSame $REFINE_TYPE REVIEW IDEA ] } {
append cmd " HKLIN \"$CURRENT_MTZ\" HKLOUT \"$NEW_MTZ\"" }
if { $MAKE_LIBRARY != "" && [file exists $MAKE_LIBRARY] } {
append cmd " LIBIN \"$MAKE_LIBRARY\""
}
if $IFTLS { append cmd " TLSIN \"$CURRENT_TLS\" TLSOUT \"$NEW_TLS\"" }
if $IFFIXTLS { append cmd " TLSIN \"$CURRENT_TLS\"" }
if { $loop == 1 && $LIBOUT != "" } {
# Handle possibility that refmac finds new monomer and exits after creating
# library file
# Is there already a file LIBOUT - find when it was created
set libout_date 0
if { [file exists $LIBOUT] } {
file stat $LIBOUT file_stat
set libout_date $file_stat(ctime)
}
append cmd " LIBOUT \"$LIBOUT\""
set status [Execute $cmd $refmac_script program_status report -noexit]
if { $status <= 0 || [regexp REVIEW $REFINE_TYPE] } {
if { $LIBOUT != "" && [file exists $LIBOUT] } {
file stat $LIBOUT file_stat
if { $file_stat(ctime) > $libout_date } {
AddOutputFile $LIBOUT $DIR_LIBOUT }
}
TerminateScript $status -report $report
}
} else {
set status [Execute $cmd $refmac_script program_status report]
}
#------------------------------------------------------------------------------
# If requested, run findwaters utility from Coot
#------------------------------------------------------------------------------
if $RUN_COOT_FW {
set findwaters [BinPath findwaters]
if { [regexp -nocase windows $::tcl_platform(os)] } { set findwaters [BinPath findwaters-real.exe] }
set COOT_PDB_W [GetTmpFileName -ext coot_pdb_$loop ]
set COOT_PDB1 [GetTmpFileName -ext coot_pdb_$loop ]
set COOT_PDB2 [GetTmpFileName -ext coot_pdb_$loop ]
DeleteFile $COOT_PDB_W
DeleteFile $COOT_PDB1
DeleteFile $COOT_PDB2
set cmd "$findwaters --pdbin \"$NEW_PDB\" --hklin \"$NEW_MTZ\" --f $DELFWT --phi $PHDELWT --pdbout \"$COOT_PDB_W\" --sigma $COOT_SIGMA_ADD"
WriteToLog " *** Starting COOT:findwaters to find new waters *** \n Using command: $cmd"
set status [Execute $cmd "" program_status report]
MergePdbFiles $COOT_PDB1 [list $NEW_PDB $COOT_PDB_W]
set cmd "$findwaters --pdbin \"$COOT_PDB1\" --hklin \"$NEW_MTZ\" --f $FWT --phi $PHWT --pdbout \"$COOT_PDB2\" --chop --sigma $COOT_SIGMA_REMOVE"
WriteToLog " *** Starting COOT:findwaters to remove poor waters *** \n Using command: $cmd"
set status [Execute $cmd "" program_status report]
DeleteFile $COOT_PDB_W
DeleteFile $COOT_PDB1
WriteToLog " *** Ending COOT:findwaters *** "
}
#-----------------------------------------------------------------------------
# Update files
#-----------------------------------------------------------------------------
if { $RUN_COOT_FW } {
set CURRENT_PDB $COOT_PDB2
} else {
set CURRENT_PDB $NEW_PDB
}
if $IFTLS { set CURRENT_TLS $NEW_TLS }
# end of external loop
}
#############################################################################
# termination
#############################################################################
HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME refmac
# If running Coot then add one final REFMAC cycle
if { $RUN_COOT_FW } {
WriteToLog "NEW_PDB: $NEW_PDB"
set cmd "[BinPath refmac5] XYZIN \"$CURRENT_PDB\" XYZOUT \"$NEW_PDB\" HKLIN \"$CURRENT_MTZ\" HKLOUT \"$NEW_MTZ\""
if { $MAKE_LIBRARY != "" && [file exists $MAKE_LIBRARY] } {
append cmd " LIBIN \"$MAKE_LIBRARY\"" }
if $IFTLS {
append cmd " TLSIN \"$CURRENT_TLS\" TLSOUT \"$NEW_TLS\""
}
if $IFFIXTLS { append cmd " TLSIN \"$CURRENT_TLS\"" }
set status [Execute $cmd $refmac_script program_status report ]
set CURRENT_PDB $NEW_PDB
if $IFTLS { set CURRENT_TLS $NEW_TLS }
}
WriteToLog "Writing final coordinates (XYZOUT) to $XYZOUT"
WriteToLog "Writing final phases (HKLOUT) to $HKLOUT"
if $IFTLS {
WriteToLog "Writing final TLS (TLSOUT) to $TLSOUT"
}
#--------------------------------------------------------------------
# generate maps
#--------------------------------------------------------------------
if { $IF_MAPOUT } {
source [SearchPath TOP scripts refmac_maps.script ]
}