gen-sfs-expand

#!/bin/sh

PDB=$1
SYMM=$2
RESOLUTION=$3
PG=$4

if [ "x$PDB" = "x" ]; then
	echo "Syntax: $0 <PDB file> <space group> [<resolution>] [<point group>]"
	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."
	exit
fi

if [ "x$SYMM" = "x" ]; then
	echo "Syntax: $0 <PDB file> <space group> [<resolution>]"
	exit
fi

if [ "x$RESOLUTION" = "x" ]; then
	echo "Resolution not given.  Using 3 Angstroms."
	RESOLUTION=3
fi

if [ "x$PG" = "x" ]; then
	echo "Point group not given.  Output will not contain symmetry information."
	PG=unknown
fi

echo "Running sfall to calculate structure factors..."
sfall XYZIN $PDB HKLOUT ${PDB}.mtz > gen-sfs.html << EOF
MODE SFCALC XYZIN
RESOLUTION $RESOLUTION 1000
FORM NGAUSS 5
SYMM $SYMM
END
EOF
if [ $? -ne 0 ]; then
	echo "Failed!  Please examine gen-sfs.html for more information."
	exit 1
fi

echo "Running cad to get the right asymmetric unit..."
cad HKLIN1 ${PDB}.mtz HKLOUT ${PDB}-sorted.mtz >> gen-sfs.html <<EOF
TITLE Sorted blah
LABIN FILE 1 E1=FC E2=PHIC
CTYPE FILE 1 E1=F  E2=P
EOF
if [ $? -ne 0 ]; then
	echo "Failed!  Please examine gen-sfs.html for more information."
	exit 1
fi

echo "Running sftools to expand reflections to P1..."
sftools >> gen-sfs.html << EOF
READ ${PDB}-sorted.mtz
EXPAND
WRITE ${PDB}-P1.mtz
STOP
EOF

echo "Converting structure factors to text..."
mtz2various hklin ${PDB}-P1.mtz hklout ${PDB}-temp.hkl >> gen-sfs.html <<EOF
LABIN H=H K=K L=L FC=FC PHIC=PHIC
OUTPUT USER '(3I6,2F9.1)'
EOF
if [ $? -ne 0 ]; then
	echo "Failed!  Please examine gen-sfs.html for more information."
	exit 1
fi

rm -f ${PDB}-P1.mtz
rm -f ${PDB}.mtz
rm -f ${PDB}-sorted.mtz

perl < ${PDB}-temp.hkl > ${PDB}.hkl << WIBBLE
use strict;

my \$line;
open(FILE, "${PDB}-temp.hkl");

printf("CrystFEL reflection list version 2.0\n");
printf("Symmetry: ${PG}\n");

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 \$intensity = \$4*\$4;  # Square to convert F->I
                my \$phase = \$5;

                printf("%4i %4i %4i %10.2f %8.2f %10.2f %7i\n",
                       \$h, \$k, \$l, \$intensity, \$phase, 0.0, 1);

        } else {
		printf(STDERR "Couldn't understand line '%s'\n", \$line);
        }

}
close(FILE);
printf("End of reflections\n");
WIBBLE

rm -f ${PDB}-temp.hkl