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Generate XDS.INP: Difference between revisions
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→The script
(→The script: rev 1.04 (Zhipu Luo)) |
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# revision 1.01 . KD 07/12/2020 ROTATION_AXIS=0 -1 0 for Pilatus3 2M, S/N 24-0118 at ID23-2 (http://www.globalphasing.com/autoproc/wiki/index.cgi?BeamlineSettings) | # revision 1.01 . KD 07/12/2020 ROTATION_AXIS=0 -1 0 for Pilatus3 2M, S/N 24-0118 at ID23-2 (http://www.globalphasing.com/autoproc/wiki/index.cgi?BeamlineSettings) | ||
# revision 1.02 . KD 11/01/2021 recognize mar555 detector as mar345 (thanks to Thomas Hauß, HZB) | # revision 1.02 . KD 11/01/2021 recognize mar555 detector as mar345 (thanks to Thomas Hauß, HZB) | ||
# revision 1.03 . Feng | # revision 1.03 . Feng Yu 18/7/2021 fix/expand information about Shanghai Synchrotron Radiation Facility (SSRF) | ||
# revision 1.04 . Zhipu Luo 13/08/2021 extract ORGX,ORGY for electron diffraction if the | # revision 1.04 . Zhipu Luo 13/08/2021 extract ORGX,ORGY for electron diffraction from SMV header if the wavelength value starts with 0.0 | ||
REVISION="1. | # revision 1.05 . KD specialcase extraction of number of images for BNL detectors E-32-0101 and E-18-0104 | ||
# revision 1.06 . KD fix URLs in output. Availability of Apple M1 processor dectris-neggia-Apple-arm64.so . LC_ALL=C . | |||
# revision 1.07 . KD, Thomas Hauß, Gleb Bourenkov 25/10/2021. Detector moved from Petra P14 to P13 | |||
# revision 1.08 . KD, Thomas Hauß, Feng Yu 7/11/2021 fix TZ in timestamps for SSRF detectors | |||
# revision 1.09 . KD, Feng Yu 7/11/2021 fix detector number BNL E-18-0121 to be E-18-0104 | |||
REVISION="1.09 (9-NOV-2021)" | |||
# | # | ||
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exit | exit | ||
fi | fi | ||
# make sure the locale does not interfere with e.g. awk calculations: | |||
LC_ALL="C";export LC_ALL | |||
# | # | ||
# defaults: | # defaults: | ||
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SEPMIN=7.0 | SEPMIN=7.0 | ||
CLUSTER_RADIUS=3.5 | CLUSTER_RADIUS=3.5 | ||
REFINE_CORRECT="CELL BEAM ORIENTATION AXIS POSITION ! Default is: refine everything" | |||
dname=`echo "$1" | xargs dirname` | dname=`echo "$1" | xargs dirname` | ||
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data_last=`cut -b $pos1-$pos2 tmp1 | tail -n1 | bc` | data_last=`cut -b $pos1-$pos2 tmp1 | tail -n1 | bc` | ||
DATA_RANGE="$data_first $data_last" | DATA_RANGE="$data_first $data_last" | ||
echo DATA_RANGE=$DATA_RANGE | |||
# set SPOT_RANGE to first half of DATA_RANGE | # set SPOT_RANGE to first half of DATA_RANGE | ||
| Line 215: | Line 224: | ||
FIRSTFRAME=`head -1 tmp1` | FIRSTFRAME=`head -1 tmp1` | ||
echo $FIRSTFRAME | grep "\.h5$" && is_h5=1 || is_h5=0 | echo $FIRSTFRAME | grep "\.h5$" && is_h5=1 || is_h5=0 | ||
# find out detector type | # find out detector type | ||
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elif [ "$DET" == "experimental-ED" ]; then | elif [ "$DET" == "experimental-ED" ]; then | ||
DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000 ! OVERLOAD is really unknown " | DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000 ! OVERLOAD is really unknown " | ||
echo --- Electron diffraction data in SMV | echo --- Electron diffraction data in SMV format! | ||
SENSOR_THICKNESS=0.01 | SENSOR_THICKNESS=0.01 | ||
sed s/\;// tmp2 > tmp1 | sed s/\;// tmp2 > tmp1 | ||
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BEAM_CENTER_Y=`grep BEAM_CENTER_Y tmp2 | sed s/BEAM_CENTER_Y=//` | BEAM_CENTER_Y=`grep BEAM_CENTER_Y tmp2 | sed s/BEAM_CENTER_Y=//` | ||
QXY=`echo "scale=1; $QX*($BEAM_CENTER_X+$BEAM_CENTER_Y)" | bc -l` | QXY=`echo "scale=1; $QX*($BEAM_CENTER_X+$BEAM_CENTER_Y)" | bc -l` | ||
if [ "$QXY" "<" "$BEAM_CENTER_X" ] ; then | if [ "$QXY" "<" "$BEAM_CENTER_X" ] ; then | ||
ORGX=`echo "scale=2; $BEAM_CENTER_Y/$QX" | bc -l` | ORGX=`echo "scale=2; $BEAM_CENTER_Y/$QX" | bc -l` | ||
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echo --- For TIMEPIX detector, please fix ROTATION_AXIS yourself! | echo --- For TIMEPIX detector, please fix ROTATION_AXIS yourself! | ||
DIRECTION_OF_DETECTOR_X_AXIS="1 0 0" | DIRECTION_OF_DETECTOR_X_AXIS="1 0 0" | ||
REFINE_CORRECT="ORIENTATION CELL AXIS BEAM ! for ED, no POSITION when CELL is refined" | |||
elif [ "$DET" == "pilatus" ]; then | elif [ "$DET" == "pilatus" ]; then | ||
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# find SENSOR_THICKNESS: | # find SENSOR_THICKNESS: | ||
SENSOR_THICKNESS=`grep thickness tmp2 | sed -e s/' | SENSOR_THICKNESS=`grep thickness tmp2 | sed -e s/'Si.* sensor, thickness'// | awk '{print $1*1000}'` | ||
# find X_RAY_WAVELENGTH: | # find X_RAY_WAVELENGTH: | ||
X_RAY_WAVELENGTH=`grep Wavelength tmp2 | sed -e s/Wavelength// -e s/A// | awk '{print $1}'` | X_RAY_WAVELENGTH=`grep Wavelength tmp2 | sed -e s/Wavelength// -e s/A// | awk '{print $1}'` | ||
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fi | fi | ||
# PETRA P14: raw data from Eiger are stored as CBF files so this is treated as Pilatus | # PETRA P14: raw data from Eiger are stored as CBF files so this is treated as Pilatus | ||
if [ | if [ "$DET_SN" == "Dectris Eiger 4M, E-08-0107" -o "$DET_SN" == "PILATUS 6M-F, S/N 60-0115-F" ] ; then | ||
rotation_axis="0 -1 0" | rotation_axis="0 -1 0" | ||
echo ROTATION_AXIS="0 -1 0" at PETRA P14 | echo ROTATION_AXIS="0 -1 0" at PETRA P14 | ||
fi | |||
# similarly, Eiger 16M at PETRA P14 until May 22, 2021 | |||
if [ "$DET_SN" == "Dectris Eiger 16M, E-32-0107" ] ; then | |||
egrep -q '^# 2020-|^# 2021-0[1-5]|^# 2021-06-[01]|^# 2021-06-2[01]' tmp2 || isatP13=1 | |||
if [ "$isatP13" == 1 ] ; then | |||
echo using the default ROTATION_AXIS=1 0 0 at PETRA P13 | |||
else | |||
rotation_axis="0 -1 0" | |||
echo ROTATION_AXIS="0 -1 0" at PETRA P14 | |||
fi | |||
fi | fi | ||
# ESRF ID23-2: | # ESRF ID23-2: | ||
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elif [ "$DET" == "eiger" ]; then | elif [ "$DET" == "eiger" ]; then | ||
nframes=`h5dump -d "/entry/instrument/detector/detectorSpecific/nimages" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | |||
DATA_RANGE="1 $nframes" | |||
SPOT_RANGE="1 `echo "scale=0; if (${nframes}<2) 1; if (${nframes}>1) ${nframes}/2"|bc -l`" | |||
# find out if HDF5 from Diamond (DLS=1) or Dectris (DLS=0) | # find out if HDF5 from Diamond (DLS=1) or Dectris (DLS=0) | ||
DLS=0 | DLS=0 | ||
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# SSRF BL17U1 and SSRF BL10U2 (Feng YU 2021-07-18) | # SSRF BL17U1 and SSRF BL10U2 (Feng YU 2021-07-18) | ||
# Eiger X 16M (S/N E-32-0111) was installed at SSRF BL17U1 from Oct 2017 to Feb 2021. After Feb 2021, it was moved back to SSRF BL10U2. | # Eiger X 16M (S/N E-32-0111) was installed at SSRF BL17U1 from Oct 2017 to Feb 2021. After Feb 2021, it was moved back to SSRF BL10U2. | ||
# 2021- | # 2021-03-01 00:00:00 time stamp is 1614528000 | ||
if [ "$SN" == "E-32-0111" ]; then | if [ "$SN" == "E-32-0111" ]; then | ||
collection_time=`h5dump -d "/entry/instrument/detector/detectorSpecific/data_collection_date" $FIRSTFRAME | grep "(0):" | awk '{print $2}' | sed -e "s/\.\(.*\)/ | collection_time=`h5dump -d "/entry/instrument/detector/detectorSpecific/data_collection_date" $FIRSTFRAME | grep "(0):" | awk '{print $2}' | sed -e "s/\.\(.*\)//g; s/\"//g"` | ||
if [ `uname -s` == "Darwin" ]; then | if [ `uname -s` == "Darwin" ]; then | ||
collection_timestamp=`date -j -f "%Y-%m-%dT%H:%M:%S | collection_timestamp=`date -j -f "%Y-%m-%dT%H:%M:%S" $collection_time +%s` | ||
elif [ `uname -s` == "Linux" ]; then | elif [ `uname -s` == "Linux" ]; then | ||
collection_timestamp=`date -d $collection_time +%s` | collection_timestamp=`date -d $collection_time +%s` | ||
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rotation_axis="-1 0 0 ! Cannot determine rotation axis. SSRF BL17U1: -1 0 0; SSRF BL02U1: 0 -1 0" | rotation_axis="-1 0 0 ! Cannot determine rotation axis. SSRF BL17U1: -1 0 0; SSRF BL02U1: 0 -1 0" | ||
fi | fi | ||
elif [ $collection_timestamp -ge 0 ] && [ $collection_timestamp -le | elif [ $collection_timestamp -ge 0 ] && [ $collection_timestamp -le 1614528000 ]; then | ||
# SSRF BL17U1 | # SSRF BL17U1 | ||
rotation_axis="-1 0 0" | rotation_axis="-1 0 0" | ||
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echo "SSRF BL02U1 (Eiger2 S 9M) with horizontal rotation axis" | echo "SSRF BL02U1 (Eiger2 S 9M) with horizontal rotation axis" | ||
fi | fi | ||
fi | |||
# revision 1.05 specialcase nframes for Eiger detectors at BNL | |||
if [ "$SN" == "E-18-0104" -o "$SN" == "E-32-0101" ]; then | |||
echo specialcase nframes for Eiger detectors at BNL: | |||
nframes=`h5dump -A -g "/entry/data" $FIRSTFRAME | grep "DATASPACE SIMPLE" | sed -e "s/,.*//" | awk '{a+=$5}END{print a}'` | |||
DATA_RANGE="1 $nframes" | |||
SPOT_RANGE="1 `echo "scale=0; if (${nframes}<2) 1; if (${nframes}>1) ${nframes}/2"|bc -l`" | |||
fi | fi | ||
fi | fi | ||
echo DATA_RANGE=$DATA_RANGE | |||
DETECTOR="EIGER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD" | DETECTOR="EIGER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD" | ||
QX=`h5dump -d "/entry/instrument/detector/x_pixel_size" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` | QX=`h5dump -d "/entry/instrument/detector/x_pixel_size" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` | ||
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! however, if the spots from COLSPOT extend to 2A then POSITION could, and if 1.5A POSITION should be refined | ! however, if the spots from COLSPOT extend to 2A then POSITION could, and if 1.5A POSITION should be refined | ||
REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS ! add POSITION if high resolution, or DETECTOR_DISTANCE inaccurate | REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS ! add POSITION if high resolution, or DETECTOR_DISTANCE inaccurate | ||
REFINE(INTEGRATE)= POSITION BEAM ORIENTATION ! AXIS CELL . If 1.5A or higher it is ok to refine CELL | REFINE(INTEGRATE)= POSITION BEAM ORIENTATION ! AXIS CELL . If 1.5A or higher it is ok to refine CELL (unless electron diffraction) | ||
REFINE(CORRECT)= $REFINE_CORRECT | |||
! parameters specifically for this detector and beamline: | ! parameters specifically for this detector and beamline: | ||
DETECTOR= $DETECTOR | DETECTOR= $DETECTOR | ||
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if [ -e /usr/local/lib64/dectris-neggia.so ]; then | if [ -e /usr/local/lib64/dectris-neggia.so ]; then | ||
echo LIB=/usr/local/lib64/dectris-neggia.so >> XDS.INP | echo LIB=/usr/local/lib64/dectris-neggia.so >> XDS.INP | ||
echo LIB= line was written to XDS.INP | echo LIB= line was written to XDS.INP . For Apple ARM64 processors, you must modify the name. | ||
else | else | ||
echo !LIB=/usr/local/lib64/dectris-neggia.so >> XDS.INP | echo !LIB=/usr/local/lib64/dectris-neggia.so >> XDS.INP | ||
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fi | fi | ||
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 Full documentation, including complete detector templates, | echo Full documentation, including complete detector templates, at xds.mr.mpg.de . | ||
echo | echo More documentation in strucbio.biologie.uni-konstanz.de/xdswiki/index.php . | ||
echo After running xds, inspect | echo After running xds, inspect at least the agreement of predicted and observed | ||
echo spots in FRAME.cbf! | |||
rm -f tmp1 tmp2 | rm -f tmp1 tmp2 | ||