#!/bin/sh

#
# Example scripts for areaimol using toxd data
#

# used to distinguish different runs in html logfile
CCP_PROGRAM_ID=run1
export CCP_PROGRAM_ID
##################################################
#
# Simple area calculation (verbose output)
#
##################################################
areaimol XYZIN $CEXAM/toxd/toxd.pdb \
         XYZOUT $CCP4_SCR/sarea1.brk <<eof-area
VERB      ! Verbose output
OUTPUT    ! Output pseudo-pdb file
END
eof-area
#
##################################################
#
# Water differences with lattice symmetry contacts
# and probe radius set to 1.6 A
#
##################################################
CCP_PROGRAM_ID=run2
areaimol XYZIN $CEXAM/toxd/toxd.pdb  <<eof-area
DIFFMODE WATER
SMODE IMOL
SYMMETRY 19
TRANS
PROBE 1.6
END
eof-area
#
##################################################
#
# Differences due to intermolecular lattice
# contacts, ignoring waters
#
##################################################
CCP_PROGRAM_ID=run3
areaimol XYZIN $CEXAM/toxd/toxd.pdb \
         XYZOUT $CCP4_SCR/sdiff1.brk <<eof-area
DIFFMODE IMOL
MODE NOHOH
OUTPUT
SYMMETRY 1
SYMMETRY 19
TRANS 2
END
eof-area
#
##################################################
#
# Area change due to absence of a residue
#
##################################################
#
# First: make an altered version of toxd by
# cutting out LYS A residues using the unix
# 'grep' command
#
grep -v 'LYS A   5' $CEXAM/toxd/toxd.pdb > $CCP4_SCR/toxd_1.pdb
#
# Then obtain the resulting area differences
#
CCP_PROGRAM_ID=run4
areaimol XYZIN $CEXAM/toxd/toxd.pdb \
         XYZIN2 $CCP4_SCR/toxd_1.pdb \
         XYZOUT $CCP4_SCR/sdiff2.brk <<eof-area
DIFFMODE COMPARE
OUTPUT
END
eof-area
#