#
#     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 $Id$
#===========================================================================
#
# patterson.script
#
#===========================================================================

# Source file with utility procedures
  source [SearchPath TOP src CCP4_utils.tcl]
  source [SearchPath TOP utils map_utils.tcl]
# Read the crystal parameters files
  ReadSymops [FileJoin [GetEnvPath CLIBD] symop.lib]
  ReadCrystalData [SearchPath TOP etc crystal.lib]

  CreateComScript  fft patterson_script

  set status [ Execute "[BinPath fft] HKLIN \"$HKLIN\" MAPOUT \"$MAPOUT\""  \
   $patterson_script program_status report]


  set PEAK_FILE [SetOutputFileRoot]_peaks.pdb
  set XYZFRC [SetOutputFileRoot]_peaks.ha

  CreateComScript peakmax peaks_script
  set cmd "[BinPath peakmax]"
  append cmd " MAPIN \"$MAPOUT\""
  append cmd " XYZOUT \"$PEAK_FILE\""
  append cmd " XYZFRC \"$XYZFRC\""
  if { $OUTPUT_XML } { 
    append cmd " XMLFILE \"$XMLFILE\"" 
  }
  set status [Execute $cmd $peaks_script program_status report ]

  AddOutputFile $PEAK_FILE PROJECT $XYZFRC PROJECT

  if { $BANALYSIS } {
#
#  Run Wilson to determine B value for the exptal data 

    set bdata ""
    set bmodel ""

# Run RWCONTENTS if required

    if { $CONTENTS_MODE == "PDB" } {
# use the GetPDBContents procedure in pdb_utils.tcl to get contents of PDB file
      source [FileJoin [GetEnvPath CCP4I_TOP] utils pdb_utils.tcl]
      GetPDBContents $CONTENTS_PDB nres contents heavy_atoms
      set N_CONTENTS 0
      foreach element $contents {
        incr N_CONTENTS
        set CONTENTS_ATOM_TYPE($N_CONTENTS) [lindex $element 0]
        set CONTENTS_ATOM_COUNT($N_CONTENTS) [lindex $element 1]
      }
    }

    set LABIN "FP SIGFP"
    set FP $F1
    set SIGFP $SIG1
    set EXCLUDE_RESOLUTION 0

    set tmplog [GetTmpFileName -ext log]

    CreateComScript wilson wilson_script

    set status [Execute "[BinPath wilson] HKLIN \"$HKLIN\"" $wilson_script \
		program_status report -copy_log $tmplog]

    if { [ReadFile $tmplog tmptext] } {
      set bdata [ExtractFromText $tmptext "Least squares straight line gives" 0 7 ] }

    DeleteFile $tmplog

#Run baverage to get the B value for the model data

    CreateComScript baverage baverage_script

    set status [Execute "[BinPath baverage] xyzin \"$XYZIN\"" $baverage_script \
                program_status report -copy_log $tmplog]


    if { [ReadFile $tmplog tmptext] } {
      set bmodel [ExtractFromText $tmptext "AVERAGE B VALUE FOR ALL ATOMS" 0 6 ] }

    DeleteFile $tmplog

    if { ![catch {set badd [expr $bdata - $bmodel]}] } {

    WriteToLog "Average B value for experimental data = $bdata
Average B value for model = $bmodel

Running aMoRe: set the Tabling parameter BADD 
(the amount to add to the Bvalue) to $badd"


    }

  }