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→‎The script: take away POSITION from REFINE(CORRECT) if electron diffraction data
Line 10: Line 10:     
== The script ==
 
== The script ==
 +
 
<pre>
 
<pre>
   Line 115: Line 116:  
# 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 0.98 . Thomas Hauß (HZB) 06/11/2020 switch Python print syntax to Python3
 
# revision 0.98 . Thomas Hauß (HZB) 06/11/2020 switch Python print syntax to Python3
REVISION="0.98 (06-Nov-2020)"
+
# 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 1.03 . 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 (13-AUG-2021)"
    
#                                                                                                             
 
#                                                                                                             
Line 168: Line 175:  
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`
Line 239: Line 247:  
  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   
  grep -q MARCONTROL tmp2 && DET=OLDMAR                  
+
  grep -q MARCONTROL tmp2 && DET=OLDMAR
 +
grep -q "WAVELENGTH=0.0" tmp2 && DET=experimental-ED                                   
 
else
 
else
 
  h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME | grep -i Eiger > /dev/null && DET=eiger
 
  h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME | grep -i Eiger > /dev/null && DET=eiger
Line 462: Line 473:  
   DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=/-/`                                                                     
 
   DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=/-/`                                                                     
 
   OSCILLATION_RANGE=`grep OMEGA_DELTA tmp2 | sed s/OMEGA_DELTA=//`   
 
   OSCILLATION_RANGE=`grep OMEGA_DELTA tmp2 | sed s/OMEGA_DELTA=//`   
   DIRECTION_OF_DETECTOR_X_AXIS="-1 0 0"                                                                 
+
   DIRECTION_OF_DETECTOR_X_AXIS="-1 0 0"  
 +
                                                                  
 +
elif [ "$DET" == "experimental-ED" ]; then
 +
  DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000  ! OVERLOAD is really unknown "
 +
  echo --- Electron diffraction data in SMV format!
 +
  SENSOR_THICKNESS=0.01                                                       
 +
  sed s/\;// tmp2 > tmp1                                                     
 +
  mv tmp1 tmp2                                                               
 +
  X_RAY_WAVELENGTH=`grep WAVELENGTH tmp2 | head -1 | sed s/WAVELENGTH=//`
 +
  NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//`
 +
  QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//`
 +
  NY=`grep SIZE2 tmp2 | tail -1 | sed s/SIZE2=//`                                           
 +
  QY=$QX 
 +
  BEAM_CENTER_X=`grep BEAM_CENTER_X tmp2 | sed s/BEAM_CENTER_X=//`
 +
  BEAM_CENTER_Y=`grep BEAM_CENTER_Y tmp2 | sed s/BEAM_CENTER_Y=//`
 +
  QXY=`echo "scale=1; $QX*($BEAM_CENTER_X+$BEAM_CENTER_Y)" | bc -l`
 +
      if [ "$QXY" "<" "$BEAM_CENTER_X" ] ; then
 +
      ORGX=`echo "scale=2; $BEAM_CENTER_Y/$QX" | bc -l`
 +
      ORGY=`echo "scale=2; $BEAM_CENTER_X/$QX" | bc -l`
 +
      else
 +
      ORGX=`echo "scale=2; $BEAM_CENTER_X/1" | bc -l`
 +
      ORGY=`echo "scale=2; $BEAM_CENTER_Y/1" | bc -l`
 +
      fi
 +
  DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=//`                                                                   
 +
  OSCILLATION_RANGE=`grep OSC_RANGE tmp2 | sed s/OSC_RANGE=//`
 +
  STARTING_ANGLE=`grep OSC_START tmp2 | sed s/OSC_START=//`
 +
  echo --- For TIMEPIX detector, please fix ROTATION_AXIS yourself!
 +
  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
Line 530: Line 569:  
         fi
 
         fi
 
       fi
 
       fi
# FIXME: insert similar code for Petra P14 here
+
# 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 [ "$DET" == "eiger" ]; then
Line 538: Line 586:  
   if [ "$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 usually not elsewhere
+
# 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 552: Line 600:  
   # STARTING_ANGLE:  the \- was introduced in version 0.91 to allow negative values :
 
   # STARTING_ANGLE:  the \- was introduced in version 0.91 to allow negative values :
 
     STARTING_ANGLE=`h5dump -d "/entry/sample/goniometer/omega_start" $FIRSTFRAME | awk '/\(0\): [\-0-9]/{print $2}'`
 
     STARTING_ANGLE=`h5dump -d "/entry/sample/goniometer/omega_start" $FIRSTFRAME | awk '/\(0\): [\-0-9]/{print $2}'`
 +
  # /entry/sample/goniometer/omega_start is missing in some eiger2 detectors (e.g. Eiger2 9M with fw version release-2020.2.1 and SIMPLON API 1.8) (Feng YU 2021-07-18)
 +
    if [ "$STARTING_ANGLE" == "" ]; then
 +
  echo "/entry/sample/goniometer/omega_start not found, try /entry/sample/goniometer/omega"
 +
  STARTING_ANGLE=`h5dump -d /entry/sample/goniometer/omega $FIRSTFRAME | grep "(0):" | head -n 1 | awk '{print $2}' | sed -e "s/,//g"`
 +
    fi
 +
    echo "STARTING_ANGLE=$STARTING_ANGLE"
 
   # 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
+
   # 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-32-0123" ]; then
 +
      rotation_axis="-1 0 0"
 +
      echo CHESS ID7B2 with inverted rotation axis
 +
    fi
 +
  # 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.
 +
# 2021-02-01 00:00:00 CST time stamp is 1612108800
 
     if [ "$SN" == "E-32-0111" ]; then
 
     if [ "$SN" == "E-32-0111" ]; then
       rotation_axis="-1 0 0"
+
       collection_time=`h5dump -d "/entry/instrument/detector/detectorSpecific/data_collection_date" $FIRSTFRAME | grep "(0):" | awk '{print $2}' | sed -e "s/\.\(.*\)/CST/g; s/\"//g"`
       echo SSRF BL17U1 with inverted rotation axis
+
      if [ `uname -s` == "Darwin" ]; then
     fi  
+
        collection_timestamp=`date -j -f "%Y-%m-%dT%H:%M:%S%Z" $collection_time +%s`
 +
      elif [ `uname -s` == "Linux" ]; then
 +
        collection_timestamp=`date -d $collection_time +%s`
 +
      else
 +
        collection_timestamp=0
 +
      fi
 +
      if [ $collection_timestamp -eq 0 ]; then
 +
        is_rotation_axis_set=1
 +
        rotation_axis=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME 2>/dev/null || is_rotation_axis_set=0`
 +
        if [ "$is_rotation_axis_set" == "1" ]; then
 +
          rotation_axis=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME | grep "(0):" | sed -e "s/^.*://; s/,//g"`
 +
          echo "The rotation axis of SSRF BL10U2 (Eiger X 16M) is $rotation_axis"
 +
        else
 +
          rotation_axis="-1 0 0    ! Cannot determine rotation axis. SSRF BL17U1: -1 0 0; SSRF BL02U1: 0 -1 0"
 +
        fi
 +
       elif [ $collection_timestamp -ge 0 ] && [ $collection_timestamp -le 1612108800 ]; then
 +
        # SSRF BL17U1
 +
        rotation_axis="-1 0 0"
 +
        echo "SSRF BL17U1 (Eiger X 16M) with inverted rotation axis"
 +
      else
 +
        # SSRF BL10U2
 +
        is_rotation_axis_set=1
 +
        rotation_axis=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME 2>/dev/null || is_rotation_axis_set=0`
 +
        if [ "$is_rotation_axis_set" == "1" ]; then
 +
          rotation_axis=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME | grep "(0):" | sed -e "s/^.*://; s/,//g"`
 +
          echo "The rotation axis of SSRF BL10U2 (Eiger X 16M) is $rotation_axis"
 +
        else
 +
          rotation_axis="0 -1 0"
 +
          echo "SSRF BL10U2 (Eiger X 16M) with vertical rotation axis"
 +
        fi
 +
      fi
 +
    fi
 +
  # SSRF BL02U1 (Feng YU 2021-07-18)
 +
  # EIGER2 S 9M SSRF BL02U1 has S/N E-18-0121
 +
    if [ "$SN" == "E-18-0121" ]; then
 +
      is_rotation_axis_set=1
 +
      rotation_axis=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME 2>/dev/null || is_rotation_axis_set=0`
 +
      if [ "$is_rotation_axis_set" == "1" ]; then
 +
        rotation_axis=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME | grep "(0):" | sed -e "s/^.*://; s/,//g"`
 +
        echo "The rotation axis of SSRF BL02U1 (Eiger2 S 9M) is $rotation_axis"
 +
      else
 +
        rotation_axis="1 0 0"
 +
        echo "SSRF BL02U1 (Eiger2 S 9M) with horizontal rotation axis"
 +
      fi
 +
     fi
 
   fi
 
   fi
 
   DETECTOR="EIGER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD"
 
   DETECTOR="EIGER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD"
Line 705: Line 810:  
  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`
Line 858: Line 964:  
! 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)=CELL BEAM ORIENTATION AXIS POSITION ! Default is: refine everything
+
REFINE(CORRECT)= $REFINE_CORRECT
 
   
! parameters specifically for this detector and beamline:
 
! parameters specifically for this detector and beamline:
 
DETECTOR= $DETECTOR
 
DETECTOR= $DETECTOR
Line 952: Line 1,057:  
!                                                  and does not seem to have any downsides.  
 
!                                                  and does not seem to have any downsides.  
 
eof
 
eof
   if [ $NX == "1028"  -a $NY == "1062" ]; then
+
   if [ "$NX" == "1028"  -a "$NY" == "1062" ]; then
 
# Eiger2 1M ; v0.97 numbers from Andreas Förster
 
# Eiger2 1M ; v0.97 numbers from Andreas Förster
 
     cat >> XDS.INP << eof
 
     cat >> XDS.INP << eof
 
UNTRUSTED_RECTANGLE=    0 1029    512  551
 
UNTRUSTED_RECTANGLE=    0 1029    512  551
 
eof
 
eof
   elif [ $NX == "1475" ]; then
+
   elif [ "$NX" == "1475" ]; then
 
     if ! grep -q Flat_field tmp2 ; then
 
     if ! grep -q Flat_field tmp2 ; then
 
     cat >> XDS.INP << eof
 
     cat >> XDS.INP << eof
Line 990: Line 1,095:  
eof
 
eof
 
     fi
 
     fi
   elif [ $NX == "2068"  -a $NY == "2162" ]; then
+
   elif [ "$NX" == "2068"  -a "$NY" == "2162" ]; then
 
# Eiger2 4M ; v0.97 numbers from Andreas Förster
 
# Eiger2 4M ; v0.97 numbers from Andreas Förster
 
     cat >> XDS.INP << eof
 
     cat >> XDS.INP << eof
Line 1,000: Line 1,105:  
  UNTRUSTED_RECTANGLE=    0 2069  1612 1651
 
  UNTRUSTED_RECTANGLE=    0 2069  1612 1651
 
eof
 
eof
   elif [ $NX == "2463" ]; then
+
   elif [ "$NX" == "2463" ]; then
 
# Pilatus 6M
 
# Pilatus 6M
 
# FIXME: here we could test if a Flat_field correction was applied like we do for 2M
 
# FIXME: here we could test if a Flat_field correction was applied like we do for 2M
Line 1,020: Line 1,125:  
UNTRUSTED_RECTANGLE=  0 2464  2315 2333
 
UNTRUSTED_RECTANGLE=  0 2464  2315 2333
 
eof
 
eof
   elif [ $NX == "3110"  -a $NY == "3269" ]; then
+
   elif [ "$NX" == "3110"  -a "$NY" == "3269" ]; then
 
# Eiger 9M
 
# Eiger 9M
 
     cat >> XDS.INP << eof
 
     cat >> XDS.INP << eof
Line 1,033: Line 1,138:  
UNTRUSTED_RECTANGLE= 0 3110 2717 2757
 
UNTRUSTED_RECTANGLE= 0 3110 2717 2757
 
eof
 
eof
   elif [ $NX == "3108"  -a $NY == "3262" ]; then
+
   elif [ "$NX" == "3108"  -a "$NY" == "3262" ]; then
 
# Eiger2 9M ; v0.97 numbers from Andreas Förster
 
# Eiger2 9M ; v0.97 numbers from Andreas Förster
 
     cat >> XDS.INP << eof
 
     cat >> XDS.INP << eof
Line 1,046: Line 1,151:  
UNTRUSTED_RECTANGLE=    0 3109  2712 2751
 
UNTRUSTED_RECTANGLE=    0 3109  2712 2751
 
eof
 
eof
   elif [ $NX == "4150" -a $NY == "4371" ]; then
+
   elif [ "$NX" == "4150" -a "$NY" == "4371" ]; then
 
# Eiger 16M
 
# Eiger 16M
 
     cat >> XDS.INP << eof
 
     cat >> XDS.INP << eof
Line 1,062: Line 1,167:  
  UNTRUSTED_RECTANGLE= 3109 3122      0 4371
 
  UNTRUSTED_RECTANGLE= 3109 3122      0 4371
 
eof
 
eof
   elif [ $NX == "4148" -a $NY == "4362" ]; then
+
   elif [ "$NX" == "4148" -a "$NY" == "4362" ]; then
 
# Eiger2 16M ; v0.97 numbers from Andreas Förster
 
# Eiger2 16M ; v0.97 numbers from Andreas Förster
 
     cat >> XDS.INP << eof
 
     cat >> XDS.INP << eof
Line 1,086: Line 1,191:  
echo BKGPIX.cbf, and the agreement of predicted and observed spots in FRAME.cbf!
 
echo BKGPIX.cbf, and the agreement of predicted and observed spots in FRAME.cbf!
 
rm -f tmp1 tmp2
 
rm -f tmp1 tmp2
 +
 
</pre>
 
</pre>
   Line 1,166: Line 1,272:  
* The script tries to interpret the header of the frames, so is currently limited to Dectris (Pilatus, Eiger), ADSC (Quantum), Rigaku (several types), MAR (CCD and image plate) detectors, and one Bruker detector. Other detectors need some values to be manually filled into XDS.INP - the relevant places are marked with XXX. These are detector properties (type, pixel size and number, min and max counts in a pixel), and experimental parameters like ROTATION_AXIS, OSCILLATION_RANGE, X-RAY_WAVELENGTH, DETECTOR_DISTANCE, and XORG, YORG. For fine-tuning of detector parameters, see the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates].
 
* The script tries to interpret the header of the frames, so is currently limited to Dectris (Pilatus, Eiger), ADSC (Quantum), Rigaku (several types), MAR (CCD and image plate) detectors, and one Bruker detector. Other detectors need some values to be manually filled into XDS.INP - the relevant places are marked with XXX. These are detector properties (type, pixel size and number, min and max counts in a pixel), and experimental parameters like ROTATION_AXIS, OSCILLATION_RANGE, X-RAY_WAVELENGTH, DETECTOR_DISTANCE, and XORG, YORG. For fine-tuning of detector parameters, see the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates].
 
* The authors have made a "best effort" to provide a XDS.INP that results in the correct sign of the anomalous signal. In the case of one detector type (internally called Rigaku SMV) this requires reversal of one detector axis, and a negative DETECTOR_DISTANCE, as is found in some of the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates]. '''For an unusual or unknown detector setup, the correct sign of the anomalous signal needs to be established and verified e.g. with a good dataset from a test crystal that has an anomalous signal.''' The authors do not take any responsibility for problems arising from incorrect sign of the anomalous signal, nor - obviously! - for any other mischief arising in or from data processing.
 
* The authors have made a "best effort" to provide a XDS.INP that results in the correct sign of the anomalous signal. In the case of one detector type (internally called Rigaku SMV) this requires reversal of one detector axis, and a negative DETECTOR_DISTANCE, as is found in some of the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates]. '''For an unusual or unknown detector setup, the correct sign of the anomalous signal needs to be established and verified e.g. with a good dataset from a test crystal that has an anomalous signal.''' The authors do not take any responsibility for problems arising from incorrect sign of the anomalous signal, nor - obviously! - for any other mischief arising in or from data processing.
* At some beamlines, the ROTATION_AXIS should be -1 0 0 ("backwards") instead of the usual 1 0 0 ("horizontal"), or even 0 1 0 ("vertical") like at one of the PETRA Hamburg BLs. We have only just started the article [[Beamline notes]], and the frame headers do not have this information, so the default chosen by [[generate_XDS.INP]] may be wrong and need manual correction.
+
* At some beamlines, the ROTATION_AXIS should be -1 0 0 ("backwards") instead of the usual 1 0 0 ("horizontal"), or even 0 1 0 ("vertical") like at one of the PETRA Hamburg BLs. The frame headers do not have this information, so the default chosen by [[generate_XDS.INP]] may be wrong and need manual correction. Pls also see the article [[Beamline notes]].
 
* Sometimes, the x- and y- values of the primary beam position recorded in the header should be used for ORGY and ORGX (i.e reversed) instead of as ORGX and ORGY. For ADSC, this has been implemented in the script for a number of beamlines.
 
* Sometimes, the x- and y- values of the primary beam position recorded in the header should be used for ORGY and ORGX (i.e reversed) instead of as ORGX and ORGY. For ADSC, this has been implemented in the script for a number of beamlines.
 +
* there are apparently several flavours of HDF5 files produced at Diamond Light Source. They differ e.g. in the naming of the header items. This means that items like NX, NY, DETECTOR_DISTANCE and number of images cannot be found by the [[generate_XDS.INP]] script. Example: The data at /dls/i04-1/data/2021/mx28114-9/processing/Lenye_Diamini/ThiL/ThiL found during the CCP4 2021 online Cape Town workshop. A workaround is to use e.g. xia2 pipeline=3dii to process these files, and - if needed - extract those items from its output files, e.g. from DEFAULT/NATIVE/SWEEP1/index/XDS.INP .
    
== See also ==
 
== See also ==
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