#!/bin/sh

set -e

# Run PDB file through PDBSET with no keywords.
# PDBSET will tidy the format where possible.
# In this case, the TER card is re-written according to full PDB specification.

pdbset XYZIN $CEXAM/toxd/toxd.pdb XYZOUT $CCP4_SCR/toxd_tidy.pdb <<EOF
END
EOF

###################  Take output from O into a form suitable for refinement

pdbset xyzin $CEXAM/toxd/toxd.pdb xyzout $CCP4_SCR/toxd_junk.pdb << eof
cell    132.02  115.21   96.20   90.00   90.00   90.00
NCODE 1
# New cell in junk.pdb, it is recommended that a spgrp is also given
spacegroup P212121
eof

if false; then

###################  Take output from Xplor into a form suitable for refinement

pdbset xyzin $CEXAM/toxd/toxd_xplor.pdb xyzout $CCP4_SCR/junk.pdb << eof
cell    132.02  115.21   96.20   90.00   90.00   90.00
spacegroup P212121
xplor
eof

fi

################### Re-label chains in toxd.pdb ##############

# First we give waters unique residue numbers

pdbset xyzin $CEXAM/toxd/toxd.pdb xyzout $CCP4_SCR/toxd_relabel1.pdb << eof
# renumber residues for waters
renumber 101 1 to 59 chain W
end
eof

# Second we do several chain name edits. Net effect should be zero in this example!

pdbset xyzin $CCP4_SCR/toxd_relabel1.pdb xyzout $CCP4_SCR/toxd_relabel2.pdb << eof
# label all chains 'q'
chain q
# change label 'q' to 'A' for 59 residues
renumber 1 1 to 59 chain q to A
# change label 'q' to 'W' or 'S' for remaining waters & sulphurs
renumber 60 60 to 64 chain q to S
renumber 101 101 to 159 chain q to W
eof

# Reset B values to a given range

pdbset xyzin $CEXAM/toxd/toxd.pdb xyzout $CCP4_SCR/toxd_bfac.pdb << eof
bfac range 10.0 50.0
end
eof

if false; then

######################## Expand dimer to tetramer, rename chains, transform
#
#  Make tetramer from dimer
#
pdbset xyzin ecrproducts268.pdb xyzout ecrprodpqrtet.pdb <<eof-1
remark  Tetramer generated from AB dimer
remark   rotated to pqr frame
remark
! Generate other dimer by z-dyad in P21212
symgen  x,y,z
symgen -x,-y,z
! Rename chains in second dimer: V & W are water chains
chain symmetry 2   A C
chain symmetry 2   B D
chain symmetry 2   V X
chain symmetry 2   W Y
! transform to molecular frame
transform -
  0.87831   0.47808   0  -
    0         0     -1.  -
 -0.47808   0.87831   0  -
 0.0  -2.713  0.0
! can also be done with shift & rotate
eof-1

fi
#