#!/bin/sh 

set -e

#
# toxd.mtz should have been created from toxd.na4 so that it
# already contains a FreeR_flag column.
# If not, then you must run FREERFLAG.
#
#   Example of refinement by refmac
#
#
#  Set parameters
#
crdin=$CEXAM/toxd/toxd.pdb
inmtz=$CEXAM/toxd/toxd.mtz
crdout=$CCP4_SCR/toxd_1.pdb
outmtz=$CCP4_SCR/toxd_refmac.mtz

#
#   Run protin  to set up geometric restraints
#   PROTCOUNTS contains the number of distances, chiral centres,etc..
#   PROTOUT    contains atomic coordinates plus all possible restraint 
#              pairings.
#
protin 				\
XYZIN $crdin \
PROTOUT $CCP4_SCR/protout.dat		\
PROTCOUNTS $CCP4_SCR/counts.dat		\
<< eof
!CHNNAME  ID=chain iden;CHNTYP=match CHNTYP;ROFFSET=start resid
CHNNAM ID  A  CHNTYP 1 ROFFSE   0
CHNNAM ID  S  CHNTYP 2 ROFFSE  59
CHNNAM ID  W  CHNTYP 3 ROFFSE   0
!CHNTYP    NTER=N-terminal resid type;CTER=C-terminal   resid type
CHNTYP 1 NTER 1 GLN 3   CTER 59 GLY 2 DISUL 0 MULP 0 CISPRO 0
CHNTYP 2 WAT
CHNTYP 3 WAT
PEPP 4 
SYMM 19
VDWRadii 1 CA 7 3.8
VDWCUT 5
END
eof

#
# Refmac step. Refine
#   PROTSCR    - an abbreviated version of PROTOUT
#                it contains atomic coordinates plus all restraint 
#                pairings for atoms which actually are present.
#
refmac \
HKLIN   $inmtz \
HKLOUT   $outmtz \
PROTOUT $CCP4_SCR/protout.dat \
PROTCOUNTS $CCP4_SCR/counts.dat \
PROTSCR $CCP4_SCR/counts.scr \
XYZIN   $crdin \
XYZOUT $crdout \
<< eor
LABIN FP=FTOXD3 SIGFP=SIGFTOXD3  FREE=FreeR_flag
LABO FC=FC PHIC=PHIC    FWT=2FOFCWT PHWT=PH2FOFCWT -
                     DELFWT=FOFCWT  PHDELWT=PHFOFCWT
REFI TYPE RESTrained
REFI RESI MLKF METH CDIR 
REFI BREF ISOTropic
!Scaling parameters
SCAL TYPE BULK   
WEIG MATR 0.5
NCYC 5
MONI FEW
BINS 20
end
eor
#
# make maps.
#
#  Sigmaa style 2mfo-dfc map with restored data
#
fft hklin $outmtz mapout $CCP4_SCR/map_2fofcwt.map \
<<eof
title Sigmaa style 2mfo-dfc map calculated with refmac coefficients
labi F1=2FOFCWT PHI=PH2FOFCWT
end
eof
#
#   Sigmaa style mfo-dfc map
#
fft hklin $outmtz mapout $CCP4_SCR/map_fofcwt.map \
<<eof
title Sigmaa style mfo-dfc map calculated with refmac coefficients
labi F1=FOFCWT PHI=PHFOFCWT
end 
eof