#!/bin/sh
# refmac-rigid.exam
# 
# A run-all script to run refmac rigid body refinement with the cubic insulin
# structure 2bn3 (Nanao & Ravelli) and the results of the run-all script
# scala-complete which will scale, merge and massage the measurements of 
# same.
#

set -e

# bug # 3192 - run-all examples produce harvest files - well to counteract
# this here set HARVESTHOME to somewhere in $CCP4_SCR

HARVESTHOME=$CCP4_SCR
export HARVESTHOME

# check that the input file - ${CCP4_SCR}/sc-exam-free.mtz - exists

if test ! -f ${CCP4_SCR}/sc-exam-free.mtz ; then
  echo "run scala-complete.exam first"
  exit 1
fi

# FIXME - residual mlkf is the default so this should probably be removed
#
# FIXME - cubic spacegroups cannot have anisotropic b factors for the 
#         bulk solvent model etc:
#         "lssc anisotropic fixbulk bbulk 200.0"
# 

# run refmac5

refmac5 \
  hklin ${CCP4_SCR}/sc-exam-free.mtz \
  hklout ${CCP4_SCR}/sc-exam-refmac5.mtz \
  xyzin ${CEXAM}/data/insulin_2bn3.pdb \
  xyzout ${CCP4_SCR}/rb-exam-refined.pdb << eof
labin FP=F SIGFP=SIGF FREE=FreeR_flag
refine type rigid 
rigidbody ncycle 10
rigidbody group 1 from 1 A to 21 A
rigidbody group 2 from 1 B to 30 B
monitor medium
eof