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Generate XDS.INP: Difference between revisions
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→The script: rev 1.02
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# revision 0.96 . KD 03/10/2020 make script echo detector serial number if inverted ROTATION_AXIS is detected. | # revision 0.96 . KD 03/10/2020 make script echo detector serial number if inverted ROTATION_AXIS is detected. | ||
# revision 0.97 . KD 19/10/2020 add UNTRUSTED_RECTANGLEs for Eiger2 (which has a few pixels less than Eiger (thanks to Andreas Förster) | # revision 0.97 . KD 19/10/2020 add UNTRUSTED_RECTANGLEs for Eiger2 (which has a few pixels less than Eiger (thanks to Andreas Förster) | ||
REVISION=" | # revision 0.98 . Thomas Hauß (HZB) 06/11/2020 switch Python print syntax to Python3 | ||
# revision 0.99 . Aaron Finke (CHESS) 07/11/2020 add ROTATION_AXIS=-1 0 0 for EIGER2 16M detector at MX beamline ID7B2 (CHESS) | |||
# revision 1.00 . Gleb Bourenkov 10/11/2020 add ROTATION_AXIS=0 -1 0 for beamline P14 (EMBL Hamburg) detectors Eiger 16M S/N E-32-0107; previously Eiger 4M S/N E-08-0107 and PILATUS 6M-F, S/N 60-0115-F | |||
# 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 (11-Jan-2021)" | |||
# | # | ||
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grep -q "^SOURCE_WAVELENGTH= *1" tmp2 && DET=dtrek | grep -q "^SOURCE_WAVELENGTH= *1" tmp2 && DET=dtrek | ||
grep -q BEAM_CENTER_X tmp2 && DET=adsc | grep -q BEAM_CENTER_X tmp2 && DET=adsc | ||
grep -q mar345 tmp2 && DET=MAR345 | grep -q mar345 tmp2 && DET=MAR345 | ||
# rev. 1.02: in one case, mar555 data could be processed pretending it is mar345, so: | |||
grep -q mar555 tmp2 && DET=MAR345 | |||
grep -q BRUKER tmp2 && grep -q CBF tmp2 && DET=Bruker-cbf | grep -q BRUKER tmp2 && grep -q CBF tmp2 && DET=Bruker-cbf | ||
grep -q CMOS1 tmp2 && DET=adsc-CMOS1 | grep -q CMOS1 tmp2 && DET=adsc-CMOS1 | ||
| Line 529: | Line 536: | ||
fi | fi | ||
fi | fi | ||
# | # PETRA P14: raw data from Eiger are stored as CBF files so this is treated as Pilatus | ||
if [ "$DET_SN" == "Dectris Eiger 16M, E-32-0107" -o "$DET_SN" == "Dectris Eiger 4M, E-08-0107" -o "$DET_SN" == "PILATUS 6M-F, S/N 60-0115-F" ] ; then | |||
rotation_axis="0 -1 0" | |||
echo ROTATION_AXIS="0 -1 0" at PETRA P14 | |||
fi | |||
# ESRF ID23-2: | |||
if [ "$DET_SN" == "PILATUS3 2M, S/N 24-0118, ESRF ID23" ] ; then | |||
rotation_axis="0 -1 0" | |||
echo ROTATION_AXIS="0 -1 0" at ESRF ID23-2 | |||
fi | |||
elif [ "$DET" == "eiger" ]; then | elif [ "$DET" == "eiger" ]; then | ||
| Line 537: | Line 553: | ||
if [ "$DLS" == 1 ]; then | if [ "$DLS" == 1 ]; then | ||
echo Eiger HDF5 from Diamond | echo Eiger HDF5 from Diamond | ||
# unfortunately h5dump 1.10 is required to get this right for the DLS .h5 files. This version is available at DLS but | # unfortunately h5dump 1.10 is required to get this right for the DLS .h5 files. This version is available at DLS but maybe not elsewhere | ||
OVERLOAD=`h5dump -d "/entry/instrument/detector/saturation_value" $FIRSTFRAME | awk '/\(0\):/{print $2}'` | OVERLOAD=`h5dump -d "/entry/instrument/detector/saturation_value" $FIRSTFRAME | awk '/\(0\):/{print $2}'` | ||
# v0.95: fix the next 2 lines by taking care of negative values with the \- , and stop after first "(0)" | # v0.95: fix the next 2 lines by taking care of negative values with the \- , and stop after first "(0)" | ||
| Line 553: | Line 569: | ||
# If rotation vector set (NeXus) | # If rotation vector set (NeXus) | ||
rotation_axis=`h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g"` | rotation_axis=`h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g"` | ||
# Eiger 16M SSRF BL17U1 | # Eiger 16M SSRF BL17U1 has S/N E-32-0111; EIGER2 16M CHESS ID7B2 has S/N E-32-0123 (A. Finke 2020-11-07) v0.99 | ||
SN=`h5dump -d "/entry/instrument/detector/detector_number" $FIRSTFRAME | awk '/\(0\): /{print $2}' | sed s/\"//g` | SN=`h5dump -d "/entry/instrument/detector/detector_number" $FIRSTFRAME | awk '/\(0\): /{print $2}' | sed s/\"//g` | ||
if [ "$SN" == "E-32-0111" ]; then | if [ "$SN" == "E-32-0111" ] || [ "$SN" == "E-32-0123" ]; then | ||
rotation_axis="-1 0 0" | rotation_axis="-1 0 0" | ||
echo SSRF BL17U1 with inverted rotation axis | echo SSRF BL17U1 or CHESS ID7B2 with inverted rotation axis | ||
fi | fi | ||
fi | fi | ||
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#let SKIP=768 | #let SKIP=768 | ||
#NX=$(od -t x -j $SKIP -N 4 $FIRSTFRAME |awk 'NR==1{print toupper($2)}'|perl -nle '@array= $_ =~/.{2}/g; print "ibase=16;obase=A;".join("",reverse @array)'|bc) | #NX=$(od -t x -j $SKIP -N 4 $FIRSTFRAME |awk 'NR==1{print toupper($2)}'|perl -nle '@array= $_ =~/.{2}/g; print "ibase=16;obase=A;".join("",reverse @array)'|bc) | ||
NX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(768);print "%.4d"%struct.unpack(">i",f.read(4))') | ! NX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(768);print "%.4d"%struct.unpack(">i",f.read(4))') | ||
NY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(772);print "%.4d"%struct.unpack(">i",f.read(4))') | ! NY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(772);print "%.4d"%struct.unpack(">i",f.read(4))') | ||
NX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(768);print("%.4d"%struct.unpack(">i",f.read(4)))') | |||
NY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(772);print("%.4d"%struct.unpack(">i",f.read(4)))') | |||
DETECTOR_DISTANCE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(344);print "-%.4f"%struct.unpack(">f",f.read(4))') | ! DETECTOR_DISTANCE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(344);print "-%.4f"%struct.unpack(">f",f.read(4))') | ||
DETECTOR_DISTANCE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(344);print("-%.4f"%struct.unpack(">f",f.read(4)))') | |||
ORGX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(540);print "%.4f"%struct.unpack(">f",f.read(4))') | ! ORGX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(540);print "%.4f"%struct.unpack(">f",f.read(4))') | ||
ORGY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(544);print "%.4f"%struct.unpack(">f",f.read(4))') | ! ORGY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(544);print "%.4f"%struct.unpack(">f",f.read(4))') | ||
ORGX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(540);print("%.4f"%struct.unpack(">f",f.read(4)))') | |||
ORGY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(544);print("%.4f"%struct.unpack(">f",f.read(4)))') | |||
OSCILLATION_RANGE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(524);phis,phie=struct.unpack(">ff",f.read(8));print "%.4f"%(phie-phis)') | ! OSCILLATION_RANGE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(524);phis,phie=struct.unpack(">ff",f.read(8));print "%.4f"%(phie-phis)') | ||
OSCILLATION_RANGE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(524);phis,phie=struct.unpack(">ff",f.read(8));print("%.4f"%(phie-phis))') | |||
QX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(776);print "%.6f"%struct.unpack(">f",f.read(4))') | ! QX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(776);print "%.6f"%struct.unpack(">f",f.read(4))') | ||
QY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(780);print "%.6f"%struct.unpack(">f",f.read(4))') | ! QY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(780);print "%.6f"%struct.unpack(">f",f.read(4))') | ||
QX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(776);print("%.6f"%struct.unpack(">f",f.read(4)))') | |||
QY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(780);print("%.6f"%struct.unpack(">f",f.read(4)))') | |||
X_RAY_WAVELENGTH=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(292);print "%.6f"%struct.unpack(">f",f.read(4))') | ! X_RAY_WAVELENGTH=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(292);print "%.6f"%struct.unpack(">f",f.read(4))') | ||
X_RAY_WAVELENGTH=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(292);print("%.6f"%struct.unpack(">f",f.read(4)))') | |||
elif [ "$DET" == "dtrek" ]; then | elif [ "$DET" == "dtrek" ]; then | ||
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DETECTOR="MAR345 MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=130000" | DETECTOR="MAR345 MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=130000" | ||
NX=`awk '/FORMAT/{print $2}' tmp2` | NX=`awk '/FORMAT/{print $2}' tmp2` | ||
NY=$NX | # next line is rev 1.02 (previously NY= $NX): | ||
NY=`awk -v NX=$NX '/FORMAT/{print $4/NX}' tmp2` | |||
QX=`awk '/PIXEL/{print $3/1000.}' tmp2` | QX=`awk '/PIXEL/{print $3/1000.}' tmp2` | ||
QY=`awk '/PIXEL/{print $5/1000.}' tmp2` | QY=`awk '/PIXEL/{print $5/1000.}' tmp2` | ||
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See also [[Generate_XDS.INP#Dependencies]] below, and the [[Installation]] article. | See also [[Generate_XDS.INP#Dependencies]] below, and the [[Installation]] article. | ||
== Copying generate_XDS.INP from XDSwiki webserver == | |||
On Linux: | |||
wget https://strucbio.biologie.uni-konstanz.de/pub/linux_bin/generate_XDS.INP | |||
chmod a+x generate_XDS.INP | |||
On Mac: | |||
curl -o generate_XDS.INP https://strucbio.biologie.uni-konstanz.de/pub/linux_bin/generate_XDS.INP | |||
chmod a+x generate_XDS.INP | |||
See also [[Installation]]. | |||
== Obtaining generate_XDS.INP from this webpage == | == Obtaining generate_XDS.INP from this webpage == | ||