From fb98f51efea510f351ef4a3d3fb75541b45d736a Mon Sep 17 00:00:00 2001
From: Chuck <chuck@cfel-chuck.desy.de>
Date: Fri, 23 May 2014 11:31:10 +0200
Subject: new reflection list format

---
 scripts/gen-sfs-expand | 22 +++++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

(limited to 'scripts')

diff --git a/scripts/gen-sfs-expand b/scripts/gen-sfs-expand
index edc3ee1d..baadbf27 100755
--- a/scripts/gen-sfs-expand
+++ b/scripts/gen-sfs-expand
@@ -3,9 +3,14 @@
 PDB=$1
 SYMM=$2
 RESOLUTION=$3
+PG=$4
 
 if [ "x$PDB" = "x" ]; then
-	echo "Syntax: $0 <PDB file> <space group> [<resolution>]"
+	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
 
@@ -19,6 +24,11 @@ if [ "x$RESOLUTION" = "x" ]; then
 	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
@@ -32,7 +42,6 @@ if [ $? -ne 0 ]; then
 	exit 1
 fi
 
-
 echo "Running cad to get the right asymmetric unit..."
 cad HKLIN1 ${PDB}.mtz HKLOUT ${PDB}-sorted.mtz >> gen-sfs.html <<EOF
 TITLE Sorted blah
@@ -71,7 +80,10 @@ use strict;
 my \$line;
 open(FILE, "${PDB}-temp.hkl");
 
-printf("  h   k   l          I    phase   sigma(I)  counts  fs/px  ss/px\\n");
+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> ) {
 
@@ -83,8 +95,8 @@ while ( \$line = <FILE> ) {
                 my \$intensity = \$4*\$4;  # Square to convert F->I
                 my \$phase = \$5;
 
-                printf("%3i %3i %3i %10.2f %8.2f %10.2f %7i %6.1f %6.1f\n",
-                       \$h, \$k, \$l, \$intensity, \$phase, 0.0, 1, 0.0, 0.0);
+                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);
-- 
cgit v1.2.3