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|
#!/bin/sh
PDB=$1
PG=$2
WAVEL=$3
RESOLUTION=$4
function show_help()
{
echo -n "Syntax: $0 <PDB file> <point group> <wavelength in Angstroms> [<resolution>]"
echo
echo "The space group and point group must be consistent, it's just"
echo "that I don't know how to convert the space group to a point"
echo "group."
}
if [ "x$PDB" = "x" ]; then
show_help
exit
fi
if [ "x$RESOLUTION" = "x" ]; then
echo "Resolution not given. Using 3 Angstroms."
RESOLUTION=3
fi
echo "Running ano_sfall.com to calculate structure factors..."
./ano_sfall.com ${PDB} ${RESOLUTION}A wave=${WAVEL}
if [ $? -ne 0 ]; then exit 1; fi
echo "Converting structure factors to text..."
mtz2various hklin ideal_ano.mtz hklout ${PDB}-temp1.hkl >> gen-sfs.html <<EOF
LABIN H=H K=K L=L DUM1=Fplus DUM2=Fminus
OUTPUT USER '(3I4,2F9.1)'
EOF
if [ $? -ne 0 ]; then exit 1; fi
rm -f ${PDB}.mtz
perl > ${PDB}-temp2.hkl << WIBBLE
use strict;
my \$line;
open(FILE, "${PDB}-temp1.hkl");
printf("CrystFEL reflection list version 2.0\n");
printf("Symmetry: %s\n", "${PG}");
printf(" h k l I phase sigma(I) nmeas\n");
while ( \$line = <FILE> ) {
if ( \$line =~ /^\s*([\d\-]+)\s+([\d\-]+)\s+([\d\-]+)\s+([\d\-\.]+)\s+([\d\-\.]+)/ ) {
my \$h = \$1;
my \$k = \$2;
my \$l = \$3;
my \$iplus = \$4*\$4; # Square to convert F->I
my \$iminus = \$5*\$5;
my \$sigi = 0.0;
printf("%4i %4i %4i %10.2f %s %10.2f %7i\n",
\$h, \$k, \$l, \$iplus, " -", \$sigi, 1);
printf("%4i %4i %4i %10.2f %s %10.2f %7i\n",
-\$h, -\$k, -\$l, \$iminus, " -", \$sigi, 1);
} else {
printf(STDERR "Couldn't understand line '%s'\n", \$line);
}
}
close(FILE);
printf("End of reflections\n");
WIBBLE
get_hkl -i ${PDB}-temp2.hkl -o ${PDB}.hkl -y ${PG} --trim-centrics
if [ $? -ne 0 ]; then exit 1; fi
rm -f ${PDB}-temp1.hkl
rm -f ${PDB}-temp2.hkl
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