#!/bin/sh
#
#  PHASE ANALYSIS is done by phistats, if you insist.
#  It will analyse any two sets of phases.
#  Here it is used to check the agreement between MIR phases
#  and PHIcalc.
#  It is probably better to do map correlation.

set -e

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

#  Calculate structure factors.
#  File toxd_mir.mtz  can be generated using mlphare.com
sfall           \
HKLIN $CCP4_SCR/toxd_phase_mir.mtz                        \
HKLOUT $CCP4_SCR/toxd_sf_mir.mtz             \
XYZIN $CEXAM/toxd/toxd.pdb                        \
<< END-sfrkall
TITL Structure factors calculed for toxd.
GRID 152 96 64    !div CELL by these should give .=. 0.7 A
MODE SFCALC XYZIN HKLIN
RESO 37 2.1
BINS  60
RSCB 8.0 2.1
SFSG 19
LABI FP=FTOXD3 SIGFP=SIGFTOXD3 
LABO ALLIN FC=FCtoxd PHIC=PHICtoxd
END-sfrkall

# Phase analysis 
#  Assign Weight 1 to FOM, Weight 2 to FC magnitude.
#
#          Analyse two sets of phases (no phase combination)

phistats hklin $CCP4_SCR/toxd_sf_mir << END
TITLE   Phase analysis
RESOLUTION  40. 2.   # Resolution limits
RANGES 10   500      #  No of bins for analysing agst S, 
LABIN FP=FTOXD3 SIGFP=SIGFTOXD3 PHIBP=PHI_mir WP=W_mir  -
      PHIB2=PHICtoxd W2=FCtoxd
END

#  Optional extra - combine these phases..
#
#         Set option to combine phase information from
# eg isomorphous  replacement with partial structure

sigmaa    \
hklin $CCP4_SCR/toxd_sf_mir hklout $CCP4_SCR/junk \
<< END-sigmaa
TITLE   Phase combination
RESOLUTION  40. 2.   # Resolution limits
RANGES 10   500      #  No of bins for analysing agst S, 
ERROR
COMBINE PART 1 

LABI FP=FTOXD3 SIGFP=SIGFTOXD3 PHIBP=PHI_mir WP=W_mir  -
HLA=HLA HLB=HLB HLC=HLC HLD=HLD  -
FC=FCtoxd PHIC=PHICtoxd

LABO PHCMB=PHICMB_all_FC  WCMB=FOMCMB_all_FC -
     DELFWT=mFo-DFc_Comb  PHDELFWT=PHmFo-DFc_Comb -
     FWT=2mFo-DFc_Comb    PHFWT=PH2mFo-DFc_Comb
END
END-sigmaa
#