#!/bin/sh

set -e

# Example of SAD phasing and substructure refinement by Refmac.

refmac5  \
HKLIN $CEXAM/data/gere.mtz \
XYZIN $CEXAM/data/gere_heavy.pdb \
XYZOUT $CCP4_SCR/gere_heavy_out.pdb \
HKLOUT $CCP4_SCR/gere_out.mtz << eor
#
# Input/output column assignments
#
LABIN   FREE=FreeR_flag  F+=F(+) SIGF+=SIGF(+) F-=F(-) SIGF-=SIGF(-)
LABO FC=FC_ref PHIC=PHIC_ref   FOM=FOM_ref PHIB=PHIB_ref
ANOM FORM SE -8.0 4.0
SOLV NO
NCYC 10
END
eor

# Example of SAD refimenent of incomplete model.

refmac5  \
HKLIN $CEXAM/data/gere.mtz \
XYZIN $CEXAM/data/gere_incompl.pdb \
XYZOUT $CCP4_SCR/gere_incompl_out.pdb \
HKLOUT $CCP4_SCR/gere_out.mtz << eor
#
# Input/output column assignments
#
LABIN   FREE=FreeR_flag  F+=F(+) SIGF+=SIGF(+) F-=F(-) SIGF-=SIGF(-)
LABO FC=FC PHIC=PHIC
ANOM FORM SE -8.0 4.0
NCYC 10
END
eor