#!/bin/sh

set -e

# NOTE: freerflag is included in the script uniqueify, and in general
# you should not need to run it on its own.

####### starting from CCP4 file (for starting from X-PLOR data with free R,
#       see also f2mtz.exam (and use `cad' afterwards) as well as
#       mtz2various.exam to go the other way)

#  Take original mtz file.
#  HKLOUT will have all items in HKLIN plus a FreeRflag
#  On average, 5% of the data has a particular flag in the range (0,19)
#  which can be used for exclusion from refinement.

freerflag HKLIN $CEXAM/toxd/toxd_old HKLOUT $CCP4_SCR/toxd_free <<+
FREERFRAC  0.05
+
#
#  If you need to extend your data generate freerflag first,
#  so that all equivalent reflections have the same status.
#
#   an example of extending native data to P1 +-h,+-k,+l
cad HKLIN1 $CCP4_SCR/toxd_free HKLOUT $CCP4_SCR/toxd_free_p1 <<+
OUTLIM SPACEGROUP P1
TITLE  Toxd data extended to P1 cell
LABIN FILE 1 E1=FTOXD3 E2=SIGFTOXD3 E3=FreeR_flag
END
+

### Example of COMPLETE keyword #####

# We take a 1.8 A dataset from rnase18.mtz and combine it with a
# freeR column from a 2.5 A dataset rnase25.mtz  In the output
# file from CAD, there are thus no freeR flags for the resolution
# range 1.8 - 2.5 A.
# We then use FREERFLAG to extend the freeR flags out to 1.8 A,
# while keeping the original ones unchanged.

cad hklin1 $CEXAM/rnase/rnase18.mtz \
    hklin2 $CEXAM/rnase/rnase25.mtz \
    hklout $CCP4_SCR/rnase_cad.mtz <<EOF 
labi file 1 E1=FNAT E2=SIGFNAT
labi file 2 E1=FreeR_flag
END
EOF

freerflag hklin $CCP4_SCR/rnase_cad.mtz hklout $CCP4_SCR/rnase_free.mtz <<EOF
COMPLETE FREE=FreeR_flag
EOF
#