From 0bcabd65823ae0d86096f0877735bea4f3b95502 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Fri, 30 Jul 2010 18:45:46 +0200
Subject: Improve scripts/create-mtz

---
 scripts/create-mtz | 57 ++++++++++++++++++++++++++++++++++++++++++++++++------
 1 file changed, 51 insertions(+), 6 deletions(-)

(limited to 'scripts/create-mtz')

diff --git a/scripts/create-mtz b/scripts/create-mtz
index 6d38f704..366125f4 100755
--- a/scripts/create-mtz
+++ b/scripts/create-mtz
@@ -1,16 +1,61 @@
 #!/bin/sh
 
-f2mtz HKLIN $1 HKLOUT $1.mtz << EOF
+OUTFILE=`echo $1 | sed -e 's/\.hkl$/.mtz/'`
+TMPFILE=`echo $1 | sed -e 's/\.hkl$/.temp.mtz/'`
+echo " Input: $1"
+echo "Output: $OUTFILE"
+if [ -e $TMPFILE -o -e $OUTFILE ]; then
+	echo "   I'm about to write to the following files, but one or more"
+	echo "   of them already exist:"
+	echo "   " $TMPFILE
+	echo "   " $OUTFILE
+	echo "   To confirm that you want to continue, which will DESTROY the"
+	echo "   current contents of these files, type 'y' and press enter."
+	read conf
+	if [ $conf != y ]; then
+		echo "Not confirmed."
+		exit 1
+	else
+		echo "Proceeding"
+	fi
+fi
 
+
+# Start by putting the CrystFEL intensities into an MTZ file
+echo "Running 'f2mtz'..."
+f2mtz HKLIN $1 HKLOUT $TMPFILE > out.html << EOF
 TITLE Reflections from CrystFEL
 NAME PROJECT wibble CRYSTAL wibble DATASET wibble
-
 CELL 281 281 165.2  90  90 120
 SYMM P63
+SKIP 1
+LABOUT H K L IMEAN SIGIMEAN
+CTYPE  H H H J     Q
+FORMAT '(F3.0,1X,F3.0,1X,F3.0,1X,F10.2,10X,F10.2)'
+EOF
+
+if [ $? -ne 0 ]; then echo "Failed."; exit; fi
+
+
+# Get the unit cell contents
+echo "Running 'rwcontents'..."
+rwcontents XYZIN ../../1JB0.pdb >> out.html << EOF
+NHOH 2.3 lowt
+EOF
+
+if [ $? -ne 0 ]; then echo "Failed."; exit; fi
 
-SKIP 2
-LABOUT H   K  L   I      SIGMA
-CTYPE  H   H  H   J      Q
-FORMAT '(F3.0, 1X, F3.0, 1X, F3.0, 1X, F10.2, 3X, F10.2, 1X, F11.2)'
 
+# Run 'truncate' to turn Is into Fs
+echo "Running 'truncate'..."
+truncate HKLIN $TMPFILE HKLOUT $OUTFILE >> out.html << EOF
+TRUNCATE NO
+LABIN H=H K=K L=L IMEAN=IMEAN SIGIMEAN=SIGIMEAN
+LABOUT H=H K=K L=L IMEAN=IMEAN SIGIMEAN=SIGIMEAN F=F SIGF=SIGF
+CONTENTS C 16938  N 3310  O 3548  MG 96  P 3  S 89  CA 1  FE 12  H 17645
 EOF
+
+if [ $? -ne 0 ]; then echo "Failed."; exit; fi
+
+rm -f $TMPFILE
+echo "Done."
-- 
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