#!/bin/sh -e
#
# This file contains two examples for using MAKEDICT to
# generate PROTIN-style dictionary entries using coordinates
# from pdb files.
#
# Example 1: a simple example using a SUL residue cut
#            out of toxd.pdb
#
# There are no planar groups, chiral centres etc.
#
makedict XYZIN $CEXAM/data/toxd_sul.pdb \
         DICT $CCP4_SCR/toxd_sul.dict \
<<eof-makedict
INPUT PDB      ! Input coordinates from pdb file
OUTPUT PROTIN  ! Output protin dictionary format
RESIDUE JNK    ! Name of residue in dictionary file; default is
               ! name in pdb file
CENTRE S       ! Centred on atom S; default is first atom
eof-makedict
#
#
# Example 2: a slightly more complicated example using
#            the first ASP residue cut from rnase.pdb
#
# First prepare a pdb file containing just the residue of
# interest:
grep 'ASP A   1' $CEXAM/rnase/rnase.pdb > $CCP4_SCR/rnase1.tmp
#
pdbset XYZIN $CCP4_SCR/rnase1.tmp XYZOUT $CCP4_SCR/rnase_asp.pdb \
<<eof-pdbset
REMARK This is the first ASP residue cut from rnase.pdb
CELL 64.900   78.320   38.790
SPACEGROUP P212121
END
eof-pdbset
#
rm -f $CCP4_SCR/rnase1.tmp
#
# Make the dictionary entry
# Here we define a planar group and a chiral group
#
makedict XYZIN $CCP4_SCR/rnase_asp.pdb \
         DICT $CCP4_SCR/rnase_asp.dict \
<<eof-makedict
INPUT PDB      ! Input coordinates from pdb file
OUTPUT PROTIN  ! Output protin dictionary format
RESIDUE JNK    ! Name of residue in dictionary file; default is
               ! name in pdb file
PLANE OD1 OD2 CG CB  ! These atoms define a plane
CHIRAL CB CG OD1 OD2 ! Define chiral group with CB at the centre
eof-makedict
#
# See the MAKEDICT documentation for a description of how to
# incorporate the resulting files into the dictionary.
#