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authorThomas White <taw@physics.org>2010-07-30 18:45:46 +0200
committerThomas White <taw@physics.org>2012-02-22 15:26:55 +0100
commit0bcabd65823ae0d86096f0877735bea4f3b95502 (patch)
treecda7abccc6ebe70cdd100b346c6fbaf166cf4082 /scripts
parent79fbfcf29a0ca1b84befab6214178e9885efde6a (diff)
Improve scripts/create-mtz
Diffstat (limited to 'scripts')
-rwxr-xr-xscripts/create-mtz57
1 files changed, 51 insertions, 6 deletions
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."