#!/bin/sh

set -e

# Run pirate on toxd mlphare output.
# 1ajr.na4 is the reference structure which provides
# the target distributions for the pirate procedure.

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

na4tomtz hklin $CEXAM/data/1ajr.na4 hklout $CCP4_SCR/ref

cpirate -stdin << eof
mtzin-ref $CCP4_SCR/ref.mtz
colin-ref-fo /*/*/[FP.F_sigF.F,FP.F_sigF.sigF]
colin-ref-hl /*/*/[FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D]
mtzin-wrk $CCP4_SCR/toxd_phase_mir.mtz
colin-wrk-fo /*/*/[FTOXD3,SIGFTOXD3]
colin-wrk-hl /*/*/[HLA,HLB,HLC,HLD]
colin-wrk-free /*/*/[FreeR_flag]
mtzout $CCP4_SCR/toxd_phase_mir_pirate1.mtz
colout pirate
ncycles 3
weight-expllk 0.5
weight-mapllk 0.1
stats-radius 9.0,3.0
skew-content 0.0,0.0
auto-content
eof

cfft -stdin << eof
mtzin $CCP4_SCR/toxd_phase_mir_pirate1.mtz
colin-fc /*/*/[pirate.F_phi.F,pirate.F_phi.phi]
mapout $CCP4_SCR/toxd_phase_mir_pirate1_fft1.map
stats
stats-radius 4.0
eof