#!/bin/sh
# awa 970408 ver 1.1
#
# mapmask - map/mask extend program 
#


# Firstly check to see if sf_calc has been
# run

set -e

if test ! -f $CCP4_SCR/toxd_fc.map; then
  echo '! running sf_calc first.' 1>&2
  echo '! see $CEXAM/unix/runnable/sf_calc .' 1>&2
  $CEXAM/unix/runnable/sf_calc
fi

# Secondly check if it worked!

if test ! -f $CCP4_SCR/toxd_fc.map; then
  echo '! sf_calc did not run correctly.' 1>&2
  echo '! run it by hand before trying this script again.' 1>&2
  exit 1
fi


#
# To Extend A Map (See Extend):
#
mapmask                                  \
mapin $CCP4_SCR/toxd_fc.map              \
mapout $CCP4_SCR/toxd_ins1.ext           \
xyzin $CEXAM/toxd/toxd.pdb << eof
BORDER 5.0
MODE mapin
eof

#
# Or:
#
mapmask                                 \
mapin $CCP4_SCR/toxd_fc.map             \
mapout $CCP4_SCR/toxd_ins2.ext << eof
XYZLIM 0 79 0 79 0 19
MODE mapin
eof

#
# To Resection A Map:
#
mapmask                                \
mapin  $CCP4_SCR/toxd_fc.map           \
mapout $CCP4_SCR/toxd_inszyx.map << eof
AXIS Z Y X
MODE mapin
eof

#
# To Rescale A Map: (r'=2r+1)
#
mapmask                               \
mapin $CCP4_SCR/toxd_fc.map           \
mapout $CCP4_SCR/toxd_insscaled.map << eof
SCALE FACTOR 2.0 1.0
MODE mapin
eof

#
# To Make A Mask From A Map (Mask Covers Region Of Map > 0.5):
#
mapmask                               \
mapin $CCP4_SCR/toxd_fc.map           \
mskout $CCP4_SCR/toxd_ins1.msk << eof
MODE mapin
eof

#
# To Make A Mask From A Map To Cover 70% Of The Unit Cell:
#
mapmask                               \
mapin $CCP4_SCR/toxd_fc.map           \
mskout $CCP4_SCR/toxd_ins2.msk << eof
MASK FRAC 0.7
MODE mapin
eof

#
# To Make A Map From A Mask:
#
mapmask                               \
mapin $CCP4_SCR/toxd_ins1.msk         \
mapout $CCP4_SCR/toxd_from_msk.map << eof
MODE mapin
eof

#
# To print out a mask section z=5 of all points above 0.9:
#
mapmask                               \
mapin $CCP4_SCR/toxd_fc.map << eof
MASK CUT 0.9
PRINT MASK Z 5 5
MODE mapin
eof

#
# To print out alternate map x-sections, scaled x100:
#
mapmask                               \
mapin $CCP4_SCR/toxd_fc.map << eof
SCALE FACTOR 100
PRINT MAP X 0 24 2
MODE mapin
eof

#
# To Make A Solvent Envelope, 2.5 Angstroms About Atoms.
#
# Use sfall to construct density for all points up to but
# not exceeding 2.5 A from atoms. Then use mapmask to select
# this region.

# Step 1: sfall

sfall                                 \
xyzin $CEXAM/toxd/toxd.pdb            \
mapout  $CCP4_SCR/junk.map << eof
MODE ATMMAP		! Calculating atom maps from coordinates. 
VDWR 2.5		! Maximum radius for which an atom is considered to 
			! contribute to the electron density (def 2.5)
SYMM P212121
eof


# Step 2: mapmask

mapmask                   \
mapin  $CCP4_SCR/junk.map \
mapout  $CCP4_SCR/bar.msk << eof
MASK CUT 0.01		! Include all reasonable electron density
MODE mapin
eof

#