#!/bin/sh -e

# Example using rnase coordinates for accessible surface
# calculation

# Comments
# --------
# surface is best run interactively; because of its poor
# input method a script is difficult to write.
#
# This is a run of surface which calculates the accessible
# area for chain A in rnase twice - once for chain A alone
# and once taking account of the presence of chain B.
#
# nb since "chain" command only recognises numbers,
# specify the chains using atom numbers

# Remove log file (if it already exists)
if test -f $CCP4_SCR/surface.log; then
  rm -f $CCP4_SCR/surface.log
fi

surface XYZIN1 $CEXAM/rnase/rnase.pdb \
        XYZOUT $CCP4_SCR/rnase_chn_a.rad <<eof-surf >> $CCP4_SCR/surface.log
# Put the first set of parameters here
#       e.g. zstep, probe etc
# This example just uses the defaults
# At the end you must issue the 'run' command to move onto
# the next set of commands
#
# use the 'subset .. calc .. serial' commands to
# select only those atoms in chain A for the area
# calculation
run
subset
calc
serial
1
751
done
next
# The 'next' starts the first area calculation
# For a second calculation issue 'run' again
# This time calculate the accessible area of chain A
# in the presence of chain B
#
# use the 'subset...done...reset' to clear the existing
# selection, before selecting chain A for calcation
# and chain B for inclusion only
# (nb would probably be better done using 2 separate
# runs of the program...)
run
subset
done
reset
subset
calc
serial
1
751
incl
serial
776
1526
done
next
# 'next' is required to do the 2nd calculation - the
# accessible area will be less than in the first because
# chain B obscures some of chain A
# 'stop' command ends the program
stop
eof-surf
#
# Use 'grep' to extract the total accessible area from
# each calculation
echo ' Total accessible areas from SURFACE are:'
grep 'all atoms in calculation' $CCP4_SCR/surface.log
exit
#