#!/bin/sh 

set -e

if test ! -f $CCP4_SCR/toxd_1.pdb; then
  echo '! run refmac.exam first' 1>&2
  exit 1
fi

lsqkab                        \
XYZIN2 $CEXAM/toxd/toxd.pdb \
XYZIN1 $CCP4_SCR/toxd_1.pdb \
XYZOUT $CCP4_SCR/rub.pdb       \
<< 'END-lsqkab' 
title I don't know what to use as a title
FIT WATOM   1 TO 10000 
MATCH 1 to  10000
output  XYZ    # ! output file XYZOUT with new coords
end
END-lsqkab

#  lsqkab being used to apply a rotation & translation
#  Alternative: use PDBSET
lsqkab			\
XYZIN2 $CEXAM/toxd/toxd.pdb \
XYZOUT $CCP4_SCR/toxd_rot_trans.pdb	\
<< 'END-lsqkab' 
title Rotating model by almn angles
ROTAT EULER  37.7 40.5 30.3
TRAN FRAC 0.36905 0.44048 0.27083
output  XYZ    # ! output file LSQOP with new coords
end
END-lsqkab

# Obtain NCS rotation/translation relating chain A to chain B
# First make a temporary copy of the original file
cp $CEXAM/rnase/rnase.pdb $CCP4_SCR/$$.pdb
lsqkab xyzin2 $CEXAM/rnase/rnase.pdb xyzin1 $CCP4_SCR/$$.pdb \
RMSTAB $CCP4_SCR/rnase_rms.tab  <<EOF
FIT RESIDUE MAIN 1 TO 96 CHAIN A
MATCH RESIDUE MAIN 1 TO 96 CHAIN B
OUTPUT  RMS    # ! output file RMSTAB with differences
END
EOF

# Remove the temporary copy
rm $CCP4_SCR/$$.pdb