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Generate XDS.INP: Difference between revisions
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→The script: improve wording
(→The script: take away POSITION from REFINE(CORRECT) if electron diffraction data) |
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# revision 1.03 . Feng YU 18/7/2021 fix/expand information about Shanghai Synchrotron Radiation Facility (SSRF) | # 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 from SMV header if the wavelength value starts with 0.0 | # 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="1.06 (15-OCT-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: | ||
| Line 205: | Line 209: | ||
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 216: | Line 221: | ||
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 [ "$DET" == "eiger" ]; then | elif [ "$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) ${nframes}/2"|bc -l`" | |||
# find out if HDF5 from Diamond (DLS=1) or Dectris (DLS=0) | # find out if HDF5 from Diamond (DLS=1) or Dectris (DLS=0) | ||
DLS=0 | DLS=0 | ||
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echo "SSRF BL02U1 (Eiger2 S 9M) with horizontal rotation axis" | echo "SSRF BL02U1 (Eiger2 S 9M) with horizontal rotation axis" | ||
fi | fi | ||
fi | |||
# revision 1.05 specialcase nframes for Eiger detectors at BNL | |||
if [ "$SN" == "E-18-0121" -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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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 | ||