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Generate XDS.INP: Difference between revisions
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This script should be in your $PATH as "generate_XDS.INP" . As the name suggests, it generates XDS.INP based on a list of frame names supplied on the commandline. | This script should be in your $PATH as "generate_XDS.INP" . As the name suggests, it generates XDS.INP based on a list of frame names supplied on the commandline. | ||
Currently works for MarCCD, ADSC and Pilatus 6M detectors. | Currently works for MarCCD, ADSC and Pilatus 6M detectors. Also supports bzip2-ed frames (leave out the .bz2 extension, as [http://strucbio.biologie.uni-konstanz.de/~dikay/XDS_html_doc/html_doc/xds_parameters.html#NAME_TEMPLATE_OF_DATA_FRAMES= documented] for XDS!). | ||
<pre> | <pre> | ||
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# revision 0.15 . KD 2/2011 - add comment for -ive sign of APS 19-ID and Australian Synchrotron rotation axis | # revision 0.15 . KD 2/2011 - add comment for -ive sign of APS 19-ID and Australian Synchrotron rotation axis | ||
# revision 0.16 . KD 3/2011 - SENSOR_THICKNESS=0.01 for ADSC and MarCCD. Add comment about SILICON= | # revision 0.16 . KD 3/2011 - SENSOR_THICKNESS=0.01 for ADSC and MarCCD. Add comment about SILICON= | ||
REVISION=0. | # revision 0.17 . KD 3/2011 - make it work for .bz2 frames; improve screen output | ||
REVISION=0.17 | |||
# | # | ||
# usage: e.g. generate_XDS.INP "frms/mydata_1_???.img" | # usage: e.g. generate_XDS.INP "frms/mydata_1_???.img" | ||
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# | # | ||
# ====== Start of script ====== | # ====== Start of script ====== | ||
echo generate_XDS.INP version $REVISION . | echo generate_XDS.INP version $REVISION . Obtain the latest version from | ||
echo http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | |||
if [ "$1" == "help" ] || [ "$1" == "-help" ] || [ "$1" == "-h" ]; then | if [ "$1" == "help" ] || [ "$1" == "-help" ] || [ "$1" == "-h" ]; then | ||
echo usage: generate_XDS.INP \"frms/mydata_1_???.img\" \(_with_ the quotation marks!\) | echo usage: generate_XDS.INP \"frms/mydata_1_???.img\" \(_with_ the quotation marks!\) | ||
echo if the frames are compressed with bzip2, leave out the .bz2 extension! | |||
exit | exit | ||
fi | fi | ||
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# and set a link if necessary | # and set a link if necessary | ||
if [ ${#1} -gt 72 ]; then | if [ ${#1} -gt 72 ]; then | ||
TMP_PATH=$(/bin/ls -C1 $1 | head -1) | TMP_PATH=$(/bin/ls -C1 $1 $1.bz2 | head -1) | ||
TMP_FILENAME=$(basename ${TMP_PATH}) | TMP_FILENAME=$(basename ${TMP_PATH}) | ||
if [ ${#TMP_FILENAME} -gt 65 ]; then | if [ ${#TMP_FILENAME} -gt 65 ]; then | ||
| Line 85: | Line 88: | ||
ln -s ${TMP_DIRNAME} images | ln -s ${TMP_DIRNAME} images | ||
fi | fi | ||
# NAME_TEMPLATE_OF_DATA_FRAMES="images/${1##/*/}" | |||
# KD 30.3.11 previous line changed to: | |||
NAME_TEMPLATE_OF_DATA_FRAMES="images/${TMP_FILENAME}" | |||
echo " Using template filename \"${NAME_TEMPLATE_OF_DATA_FRAMES}\"" | echo " Using template filename \"${NAME_TEMPLATE_OF_DATA_FRAMES}\"" | ||
fi | fi | ||
| Line 92: | Line 97: | ||
# list frames matching the wildcards in NAME_TEMPLATE_OF_DATA_FRAMES | # list frames matching the wildcards in NAME_TEMPLATE_OF_DATA_FRAMES | ||
# don't accept the "direct beam" shot at SLS/Pilatus PX-I and PX-II | # don't accept the "direct beam" shot at SLS/Pilatus PX-I and PX-II | ||
/bin/ls -C1 $1 | egrep -v "_00000.cbf|_000.img" > tmp1 || exit 1 | /bin/ls -C1 $1 $1.bz2 | egrep -v "_00000.cbf|_000.img" > tmp1 || exit 1 | ||
# we can continue - the frames are found | # we can continue - the frames are found | ||
# set upper limit of DATA_RANGE to number of frames (see "limitations" above) | # set upper limit of DATA_RANGE to number of frames (see "limitations" above) | ||
| Line 109: | Line 112: | ||
# find out detector type | # find out detector type | ||
DET=XXX | DET=XXX | ||
FIRSTFRAME=`head -1 tmp1` | |||
strings | echo $FIRSTFRAME | grep -q bz2 && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1 | ||
strings | strings $FIRSTFRAME | egrep -q 'marccd|Corrected' && DET=mccd | ||
strings $FIRSTFRAME | grep -q PILATUS && DET=pilatus | |||
strings $FIRSTFRAME | grep -q BEAM_CENTER_X && DET=adsc | |||
# identify other detector types in the same way (MAR IP would be straightforward) | # identify other detector types in the same way (MAR IP would be straightforward) | ||
| Line 122: | Line 127: | ||
# find parameters of first frame | # find parameters of first frame | ||
elif [ "$DET" == "mccd" ]; then | elif [ "$DET" == "mccd" ]; then | ||
echo Data from a MarCCD detector | |||
DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500" | DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500" | ||
SENSOR_THICKNESS=0.01 | SENSOR_THICKNESS=0.01 | ||
# use first frame of dataset to obtain parameters | # use first frame of dataset to obtain parameters | ||
# offsets are documented; values can be find in mccd_xdsparams.pl script | # offsets are documented; values can be find in mccd_xdsparams.pl script | ||
let SKIP=1024+80 | let SKIP=1024+80 | ||
NX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $ | NX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
let SKIP=$SKIP+4 | let SKIP=$SKIP+4 | ||
NY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $ | NY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
let SKIP=1720 | let SKIP=1720 | ||
DETECTOR_DISTANCE=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $ | DETECTOR_DISTANCE=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
DETECTOR_DISTANCE=`echo "scale=3; $DETECTOR_DISTANCE/1000" | bc -l` | DETECTOR_DISTANCE=`echo "scale=3; $DETECTOR_DISTANCE/1000" | bc -l` | ||
let SKIP=1024+256+128+256+4 | let SKIP=1024+256+128+256+4 | ||
ORGX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $ | ORGX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
ORGX=`echo "scale=2; $ORGX/1000" | bc -l ` | ORGX=`echo "scale=2; $ORGX/1000" | bc -l ` | ||
let SKIP=$SKIP+4 | let SKIP=$SKIP+4 | ||
ORGY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $ | ORGY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
ORGY=`echo "scale=2; $ORGY/1000" | bc -l ` | ORGY=`echo "scale=2; $ORGY/1000" | bc -l ` | ||
let SKIP=1024+256+128+256+44 | let SKIP=1024+256+128+256+44 | ||
PHISTART=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $ | PHISTART=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
let SKIP=1024+256+128+256+76 | let SKIP=1024+256+128+256+76 | ||
PHIEND=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $ | PHIEND=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
OSCILLATION_RANGE=`echo "scale=3; ($PHIEND-($PHISTART))/1000" | bc -l` | OSCILLATION_RANGE=`echo "scale=3; ($PHIEND-($PHISTART))/1000" | bc -l` | ||
let SKIP=1024+256+128+256+128+4 | let SKIP=1024+256+128+256+128+4 | ||
QX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $ | QX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
QX=`echo "scale=10; $QX/1000000" |bc -l ` | QX=`echo "scale=10; $QX/1000000" |bc -l ` | ||
let SKIP=$SKIP+4 | let SKIP=$SKIP+4 | ||
QY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $ | QY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
QY=`echo "scale=10; $QY/1000000" |bc -l ` | QY=`echo "scale=10; $QY/1000000" |bc -l ` | ||
let SKIP=1024+256+128+256+128+128+12 | let SKIP=1024+256+128+256+128+128+12 | ||
X_RAY_WAVELENGTH=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $ | X_RAY_WAVELENGTH=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
X_RAY_WAVELENGTH=`echo "scale=5; $X_RAY_WAVELENGTH/100000" | bc -l` | X_RAY_WAVELENGTH=`echo "scale=5; $X_RAY_WAVELENGTH/100000" | bc -l` | ||
| Line 176: | Line 181: | ||
DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000" | DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000" | ||
echo | echo Data from ADSC detector. Obtaining ORGX, ORGY depends on beamline setup: | ||
SENSOR_THICKNESS=0.01 | SENSOR_THICKNESS=0.01 | ||
strings | strings $FIRSTFRAME | sed s/\;// > tmp2 | ||
# find X_RAY_WAVELENGTH: | # find X_RAY_WAVELENGTH: | ||
| Line 195: | Line 200: | ||
ORGX=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l ` | ORGX=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l ` | ||
ORGY=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l ` | ORGY=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l ` | ||
echo | echo - at ESRF BLs use: ORGX=$ORGX ORGY=$ORGY | ||
# this 2nd alternative convention should be used at the following beamlines (pls complete the list): ALS 5.0.3, ... | # this 2nd alternative convention should be used at the following beamlines (pls complete the list): ALS 5.0.3, ... | ||
ORGX=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l ` | ORGX=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l ` | ||
ORGY=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l ` | ORGY=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l ` | ||
echo | echo - at e.g. ALS 5.0.3 use: ORGX=$ORGX ORGY=$ORGY | ||
# this 3rd alternative convention should be used at the following beamlines (pls complete the list): ALS 8.2.2, ... | # this 3rd alternative convention should be used at the following beamlines (pls complete the list): ALS 8.2.2, ... | ||
ORGX=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l ` | ORGX=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l ` | ||
ORGY=`echo "scale=1; $NX-$BEAM_CENTER_Y/$QX" | bc -l ` | ORGY=`echo "scale=1; $NX-$BEAM_CENTER_Y/$QX" | bc -l ` | ||
echo | echo - at e.g. ALS 8.2.2 use: ORGX=$ORGX ORGY=$ORGY - this is written to XDS.INP | ||
# the latter alternative is written into the generated XDS.INP ! You have to correct this manually in XDS.INP, or adjust this script. | # the latter alternative is written into the generated XDS.INP ! You have to correct this manually in XDS.INP, or adjust this script. | ||
# find DETECTOR_DISTANCE and OSCILLATION_RANGE: | # find DETECTOR_DISTANCE and OSCILLATION_RANGE: | ||
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SENSOR_THICKNESS=0.32 | SENSOR_THICKNESS=0.32 | ||
NX=2463 NY=2527 QX=0.172 QY=0.172 | NX=2463 NY=2527 QX=0.172 QY=0.172 | ||
echo | echo Data from a Pilatus detector | ||
head -50 | head -50 $FIRSTFRAME | sed s/#//> tmp2 | ||
# find X_RAY_WAVELENGTH: | # find X_RAY_WAVELENGTH: | ||
| Line 256: | Line 261: | ||
UNIT_CELL_CONSTANTS= 70 80 90 90 90 90 ! put correct values if known | UNIT_CELL_CONSTANTS= 70 80 90 90 90 90 ! put correct values if known | ||
INCLUDE_RESOLUTION_RANGE=50 0 ! after CORRECT, insert high resol limit; re-run CORRECT | INCLUDE_RESOLUTION_RANGE=50 0 ! after CORRECT, insert high resol limit; re-run CORRECT | ||
FRIEDEL'S_LAW=FALSE ! This acts only on the CORRECT step | FRIEDEL'S_LAW=FALSE ! This acts only on the CORRECT step | ||
| Line 293: | Line 297: | ||
eof | eof | ||
echo XDS.INP is ready for use. The file has only the most important keywords. | echo XDS.INP is ready for use. The file has only the most important keywords. | ||
echo After running xds, inspect at least BKGPIX.cbf and FRAME.cbf | echo Full documentation, including complete detector templates, is at | ||
echo http://www.mpimf-heidelberg.mpg.de/~kabsch/xds . More documentation in XDSwiki | |||
echo After running xds, inspect, using XDS-Viewer, at least the beamstop mask in | |||
echo BKGPIX.cbf, and the agreement of predicted and observed spots in FRAME.cbf! | |||
rm -f tmp1 tmp2 | rm -f tmp1 tmp2 | ||
</pre> | </pre> | ||