#!/bin/sh
#
#  Calculations leading up to map correlations.
# Need two maps, and if you want to tabulate the results 
# residue by residue, a third "map" output by sfall which 
# flags each grid point with the residue which makes the 
# largest contribution to it.
#  Warning. All grids MUST BE THE SAME!!
#  It is probably sensible if you want results tabulated according
# to residue to make this a fine grid, the sfall one should be OK.
#  Here is a set of command files to check the map correlation of 
# a structure after refinement to the MIR map,
#  and to work out real space R factors.
#  For map correlation we use 1) The MIR map ( should be dm'ed map)
#                             2) An "FC" map 
#               and           3) the sfall RESMOD map.

#  For Real space R factors we also need the FO map phased by the PHIcalc.
#  Here we are getting correlations between final coordinates, and initial ones

set -e

if test ! -f $CCP4_SCR/toxd_phase_mir.mtz; then
  echo "! run the mlphare procedure first" 1>&2
  exit 1
fi

########################################################################
#  Generate atom map with flags for each residue from FINAL coordinates
########################################################################
sfall    			\
xyzin $CEXAM/toxd/toxd.pdb \
               mapout $CCP4_SCR/last.map \
<< END-sfall 
TITL Toxd Atom map from final coordinates
GRID 152 96 64
MODE ATMMAP RESMOD
SYMM 19
FORM NGAU 2
END
END-sfall
#
########################################################################
#  Calculate sfs for FINAL coordinates - 
#   Simlest to append output FC and PHIC to MIR mtz file which contains
#  MIR phase information, also useful for different map generation.
########################################################################
sfall    			\
xyzin $CEXAM/toxd/toxd.pdb \
               hklin $CCP4_SCR/toxd_phase_mir.mtz  \
               hklout $CCP4_SCR/toxd_phase_mir_sflast.mtz    \
<< END-sfall 
TITL Toxd Sfs for FINAL coordinates.
GRID 152 96 64
MODE SFCALC XYZIN HKLIN
RESO 40.0 1.5
RSCB 5.0 1.5
BRESET 1.5
BINS 20
SFSG 19
FORM NGAU 2
BADD 0
LABI FP=FTOXD3 SIGFP=SIGFTOXD3
LABO ALLIN FC=FC_last PHIC=AC_last
END
END-sfall
#
# Calculate maps:
#  For real space R factor I need Fo and Fc maps..
# Fo map phased on original coordinates.
#
########################################################################
# Fo map from final coordinates.  (used for Real Space R factor)
########################################################################
#
fft    			\
               mapout $CCP4_SCR/folast.map    \
               hklin $CCP4_SCR/toxd_phase_mir_sflast.mtz    \
<< END-fft 
TITL Toxd  1.6A FOlast  map
GRID 152 96 64
XYZLIM 0 151 0 95 0 16
RESO 40.0 3.0
LABI F1=FTOXD3 PHI=AC_last
END
END-fft
#
#
########################################################################
# Fc map from final coordinates.
########################################################################
#
fft    			\
               mapout $CCP4_SCR/fclast.map    \
               hklin $CCP4_SCR/toxd_phase_mir_sflast.mtz    \
<< END-fft 
TITL Toxd  1.6A FClast  map
GRID 152 96 64
XYZLIM 0 151 0 95 0 16
RESO 20.0 3.0
LABI F1=FC_last PHI=AC_last
END
END-fft
########################################################################
#  mir map
########################################################################
fft    			\
               mapout $CCP4_SCR/fomir.map    \
               hklin $CCP4_SCR/toxd_phase_mir_sflast.mtz    \
<< END-fft 
TITL Toxd  2.5A Mir map
GRID 152 96 64
XYZLIM 0 151 0 95 0 16
RESO 20.0 3.0
LABI F1=FTOXD3 PHI=PHI_mir W=W_mir
END
END-fft
#

#
########################################################################
#  Correlation residue by residue of final coordinates with mir map
########################################################################
overlapmap    			\
               mapin1 $CCP4_SCR/fomir.map    \
               mapin2 $CCP4_SCR/fclast.map    \
               mapin3 $CCP4_SCR/last.map \
<< END-fft 
CORR RESI
END
END-fft
#
########################################################################
#  Real space R factor residue by residue of final coordinates 
########################################################################
overlapmap    			\
               mapin1 $CCP4_SCR/folast.map    \
               mapin2 $CCP4_SCR/fclast.map    \
               mapin3 $CCP4_SCR/last.map \
<< END-fft 
REAL SPACE 
END
END-fft
#