#!/bin/csh -f
#  Prepare a P1 map to calculate "model" structure factors for 
#   molecular replacement
#  We need 
#  1) A mask covering only one molecule in this expanded cell.
#  Can use coordinates to generate a mask in P1 cell.
#  (Could use bones2pdb to produce a dummy coordinate file from the
#  chosen density for a molecule.)
#  Or a averaging mask generated however  could be padded with zeros 
#    to cover a P1 cell. (See dm_ncs_averaging.doc for suggestions on 
#    getting this)
#     mama2ccp4 takes MAMA/O style masks into the required format.
#
#  2) the model map expanded to fill p1 cell, in the correct
#      orientation of sfall - SFSG 1.
#  This requires AXIS Z X Y, XYZLIM 0 to NX-1, 0 to NY-1,0 to NZ-1
#  MAPSYM = 1
#
#  3) the map produced by OVERLAPMAP which will only include points
#     from the protein map flagged by the mask 
#  4) A set of P1 structure factors.
#
#xyzin ~/gmt/cycle9_o.pdb  \
ncsmask \
mskin  /y/people/cowtan/temp3/gmto.msk \
mskout $SCRATCH/gmto_p1.msk \
<< 'END' 
xyzlim  0 47   0 71   0 95
AXIS Z X Y
SYMM 1
'END'
#
#
#  MAPMASK to extend protein map  to  cover whole cell 
#                   0 to NX-1, 0 to NY-1,0 to NZ-1
#  This will guarantee that complete molecules are embedded in
# the map.
#  Also need to change axis order to Z X Y for sfall P1 sfs
mapmask    \
mapin /y/people/cowtan/temp3/dmgmt.map \
MAPOUT  $SCRATCH/dmgmt_p1.map  \
<< 'END' 
xyzlim  0 47   0 71   0 95 
AXIS Z X Y
end
'END'
#   Cut out points not covered by mask
overlapmap \
MAPIN1  $SCRATCH/gmto_p1.msk  \
MAPIN2  $SCRATCH/dmgmt_p1.map  \
MAPOUT  $SCRATCH/junk.map  \
<< 'END' 
MAP INCLUDE
END
'END'
#

# Extend needed to  change map header symmetry. to P1 
#   (sfall gets upset otherwise)
extend    \
MAPIN  $SCRATCH/junk.map  \
mapout $SCRATCH/cutout_p1.map \
<< 'END' 
xyzlim  0 47   0 71   0 95 
mapsymm 1
end
'END'

#  Read in map to calculate "model" structure factors.
s:
sfall           \
HKLOUT $SCRATCH/cutout_p1.mtz   \
mapin $SCRATCH/cutout_p1.map \
<< 'END-sfrkall'
TITL  calculating structure factors from "Fc" map
MODE SFCALC MAPIN 
RESO 37 3.1
BINS  60
SFSG 1
LABO FC=FC PHIC=AC
'END-sfrkall'