#!/bin/sh

if test ! -f $CCP4_SCR/toxd_phase_mir_pirate1.mtz; then
  echo '! Run cpirate.exam first' 1>&2
  exit 1
fi

##############################################################
#  example 1
#  Reduced set of options
#
cbuccaneer -stdin << eof
mtzin-ref $CLIBD/reference_structures/reference-1tqw.mtz
pdbin-ref $CLIBD/reference_structures/reference-1tqw.pdb
mtzin-wrk $CCP4_SCR/toxd_phase_mir_pirate1.mtz
pdbout-wrk $CCP4_SCR/toxd_phase_mir.pdb
colin-wrk-fo /NATIVE/NATIVE/[FTOXD3,SIGFTOXD3]
colin-wrk-hl /*/*/[pirate.ABCD.A,pirate.ABCD.B,pirate.ABCD.C,pirate.ABCD.D]
find
grow
join
link
prune
eof

#  remove the next line if you require all the examples
exit

##############################################################
#  example 2
#  use the sequence for sequencing (proper use)
#
cbuccaneer -stdin << eof
mtzin-ref $CLIBD/reference_structures/reference-1tqw.mtz
pdbin-ref $CLIBD/reference_structures/reference-1tqw.pdb
mtzin-wrk $CCP4_SCR/toxd_phase_mir_pirate1.mtz
pdbout-wrk $CCP4_SCR/toxd_phase_mir.pdb
seqin-wrk $CEXAM/toxd/toxd.seq
colin-wrk-fo /NATIVE/NATIVE/[FTOXD3,SIGFTOXD3]
colin-wrk-hl /*/*/[pirate.ABCD.A,pirate.ABCD.B,pirate.ABCD.C,pirate.ABCD.D]
find
grow
join
link
sequence
correct
filter
prune
rebuild
eof