#!/bin/sh

set -e

# An example of a map cutting procedure, e.g. for use in a
# molecular replacement search.

# I'm not entirely sure if this is a sensible example,
# but so far it's our only runnable test of maprot

# The basic idea is to cut out the part of the 3fo2fc map
# which covers one molecule, and place it in a virtual cell

if test ! -f $CCP4_SCR/3fo2fc.map; then
  echo '! Run 3fo2fcmap first' 1>&2
  exit 1
fi

# Start with 3fo2fc.map from 3fo2fcmap example.
# This map has true spacegroup and cell, and covers 1 asymmetric unit

# Create mask covering just one molecule

# select protein only
pdbset XYZIN $CEXAM/toxd/toxd.pdb XYZOUT $CCP4_SCR/toxd_protein.pdb << eof
SELECT CHAIN A 
eof

# Now make mask in P1
ncsmask xyzin $CCP4_SCR/toxd_protein.pdb mskout $CCP4_SCR/toxd.msk << eof
eof

# change the extent of MAPIN to match that of MAPLIM
mapmask MAPIN $CCP4_SCR/3fo2fc.map MAPLIM $CCP4_SCR/toxd.msk MAPOUT $CCP4_SCR/toxd_1.map <<EOF
XYZLIM MATCH
EOF

# transfer density from WRKIN into a virtual 75A cell, output to CUTOUT
maprot WRKIN $CCP4_SCR/toxd_1.map MSKIN $CCP4_SCR/toxd.msk CUTOUT $CCP4_SCR/toxd_cut.map <<EOF
MODE TO
CELL XTAL 75.0 75.0 75.0 90 90 90
GRID XTAL 80 80 80
AVERAGE
ROTATE POLAR 0.0 0.0 0.0
TRANS 0.0 0.0 0.0
EOF
#