Generate XDS.INP: Difference between revisions

Jump to navigation Jump to search

Generate XDS.INP (view source)

Revision as of 12:18, 6 June 2022

4,670 bytes added ,  6 June 2022
m
→‎System-wide or personal installation
mNo edit summary
(31 intermediate revisions by the same user not shown)
Line 120: Line 120:
# 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 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="1.03 (22-Jul-2021)"
# 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 1.05 . 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 1.10 . KD NeXus header for Eiger
# revision 1.11 . KD / Helena Taberman ROTATION_AXIS=-1 0 0 for Eiger .cbf data from Petra P14
# revision 1.12 . KD / Helena Taberman correct rev 1.11 to be 0 -1 0
# revision 1.13 . KD variables for /usr/local/lib64/dectris-neggia.so and durin-plugin.so . Remove h5dump error messages.
REVISION="1.13 (04-Jun-2022)"


#                                                                                                             
#                                                                                                             
Line 131: Line 141:
# - for ADSC detectors, there are at least three ways to obtain ORGX and ORGY values from the header (see below);
# - for ADSC detectors, there are at least three ways to obtain ORGX and ORGY values from the header (see below);
# - the same might be a problem for MAR headers, too (not sure about this)  
# - the same might be a problem for MAR headers, too (not sure about this)  
# - on Mac OS X, the Xcode command line tools (from https://developer.apple.com/download/more/) are needed.                             
# - on macOS, the "Command Line Tools for Xcode" (from https://developer.apple.com/download/more/) are needed.                             
#                                                                                                                 
#                                                                                                                 
# notes for debugging of the script:                                                                             
# notes for debugging of the script:                                                                             
# - add the -x option to the first line, to see where an error occurs                                             
# - add the -x option to #!/bin/bash in first line, to see where an error occurs                                             
# - comment out the removal of tmp1 and tmp2 in the last line                                                     
# - comment out the removal of tmp1 and tmp2 in the last line                                                     
#                                                                                                                 
#                                                                                                                 
Line 145: Line 155:
   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 168: Line 180:
# default DIRECTION_OF_DETECTOR_X-AXIS
# default DIRECTION_OF_DETECTOR_X-AXIS
DIRECTION_OF_DETECTOR_X_AXIS="1 0 0"
DIRECTION_OF_DETECTOR_X_AXIS="1 0 0"
# default DIRECTION_OF_DETECTOR_Y-AXIS
DIRECTION_OF_DETECTOR_Y_AXIS="0 1 0"
# default FRACTION_OF_POLARIZATION
# default FRACTION_OF_POLARIZATION
pol_frac=0.98
pol_frac=0.98
Line 174: Line 188:
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 203: Line 218:
  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 214: Line 230:
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
if [ "$is_h5" == 1 ]; then
# nframes=`h5dump -A -g "/entry/data" $FIRSTFRAME | grep "DATASPACE  SIMPLE" | sed -e "s/,.*//" | awk '{a+=$5}END{print a}'`
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) ${nframes}/2"|bc -l`"
fi
echo DATA_RANGE=$DATA_RANGE


# find out detector type
# find out detector type
Line 250: Line 257:
  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 470: Line 478:
   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"                                                                 
   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 487: Line 523:


       # find SENSOR_THICKNESS:
       # find SENSOR_THICKNESS:
       SENSOR_THICKNESS=`grep thickness tmp2 | sed -e s/'Silicon sensor, thickness'// | awk '{print $1*1000}'`
       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 $1}'`             
Line 539: Line 575:
       fi
       fi
# PETRA P14: raw data from Eiger are stored as CBF files so this is treated as Pilatus
# PETRA P14: raw data from Eiger are stored as CBF files so this is treated as Pilatus
       if [ "$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
       if [ "$DET_SN" == "Dectris Eiger 4M, E-08-0107" -o "$DET_SN" == "PILATUS 6M-F, S/N 60-0115-F" \
                                        -o "$DET_SN" == "Dectris EIGER2 CdTe 16M, E-32-0129" ] ; then
         rotation_axis="0 -1 0"
         rotation_axis="0 -1 0"
         echo ROTATION_AXIS="0 -1 0" at PETRA P14
         echo ROTATION_AXIS="0 -1 0" at PETRA P14
      fi
# similarly, Eiger 16M at PETRA P14 until May 22, 2021
      if [ "$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:
Line 550: Line 597:


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`"
SN=`h5dump -d "/entry/instrument/detector/detector_number" $FIRSTFRAME | awk '/\(0\): /{print $2}' | sed s/\"//g`
echo detector serial number is $SN
# 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
Line 563: Line 616:
   # 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"`
   # the above gives -1 0 0 for DLS data instead of the correct 1 0 0, so commented out for now
   # the above gives -1 0 0 for DLS data instead of the correct 1 0 0, so commented out for now
  # comment while implementing rev 1.10: this is because the DLS headers are NeXus, so DIRECTION_OF_DETECTOR_X/Y_AXIS must be adjusted.
   else
   else
     echo Eiger HDF5 from Dectris
     echo Eiger HDF5 from Dectris
Line 568: Line 622:
     OSCILLATION_RANGE=`h5dump -d "/entry/sample/goniometer/omega_range_average" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'`
     OSCILLATION_RANGE=`h5dump -d "/entry/sample/goniometer/omega_range_average" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'`
   # 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 2>/dev/null | awk '/\(0\): [\-0-9]/{print $2}'`
   # /entry/sample/goniometer/omega_start is missing in some eiger2 detectors (e.g. Eiger2 9M with fw version release-2020.2.1 and SIMPLON API 1.8) (Feng YU 2021-07-18)
   # /entry/sample/goniometer/omega_start is missing in some eiger2 detectors (e.g. Eiger2 9M with fw version release-2020.2.1 and SIMPLON API 1.8) (Feng YU 2021-07-18)
     if [ "$STARTING_ANGLE" == "" ]; then
     if [ "$STARTING_ANGLE" == "" ]; then
  echo "/entry/sample/goniometer/omega_start not found, try /entry/sample/goniometer/omega"
  echo "/entry/sample/goniometer/omega_start not found, trying /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"`
  STARTING_ANGLE=`h5dump -d /entry/sample/goniometer/omega $FIRSTFRAME | grep "(0):" | head -n 1 | awk '{print $2}' | sed -e "s/,//g"`
     fi
     fi
     echo "STARTING_ANGLE=$STARTING_ANGLE"
     echo "STARTING_ANGLE=$STARTING_ANGLE"
   # If rotation vector set (NeXus)
   # If rotation axis 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"`
   # EIGER2 16M CHESS ID7B2 has S/N E-32-0123 (A. Finke 2020-11-07) v0.99
   # 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 $2}' | sed s/\"//g`
     if [ "$SN" == "E-32-0123" ]; then
     if [ "$SN" == "E-32-0123" ]; then
       rotation_axis="-1 0 0"
       rotation_axis="-1 0 0"
Line 585: Line 638:
   # SSRF BL17U1 and SSRF BL10U2 (Feng YU 2021-07-18)
   # SSRF BL17U1 and SSRF BL10U2 (Feng YU 2021-07-18)
   # Eiger X 16M (S/N E-32-0111) was installed at SSRF BL17U1 from Oct 2017 to Feb 2021. After Feb 2021, it was moved back to SSRF BL10U2.
   # Eiger X 16M (S/N E-32-0111) was installed at SSRF BL17U1 from Oct 2017 to Feb 2021. After Feb 2021, it was moved back to SSRF BL10U2.
# 2021-02-01 00:00:00 CST time stamp is 1612108800
# 2021-03-01 00:00:00 time stamp is 1614528000
     if [ "$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/\.\(.*\)/CST/g; s/\"//g"`
       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%Z" $collection_time +%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`
Line 604: Line 657:
           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 1612108800 ]; then
       elif [ $collection_timestamp -ge 0 ] && [ $collection_timestamp -le 1614528000 ]; then
         # SSRF BL17U1
         # SSRF BL17U1
         rotation_axis="-1 0 0"
         rotation_axis="-1 0 0"
Line 634: Line 687:
       fi
       fi
     fi
     fi
# revision 1.05 specialcase nframes for Eiger detectors at BNL
    if [ "$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
# rev 1.10: check for NeXus header. If found, its geometry will overwrite any rotation_axis set until here.
  NeXus=0
  h5dump -d "/entry/definition" $FIRSTFRAME 2>/dev/null | grep -q NXmx && NeXus=1
  if [ "$NeXus" == "1" ]; then
    echo NeXus header found. This defines DIRECTION_OF_DETECTOR_X/Y-AXIS and ROTATION_AXIS.
    DIRECTION_OF_DETECTOR_X_AXIS=$(h5dump -d "/entry/instrument/detector/module/fast_pixel_direction" $FIRSTFRAME 2>/dev/null | grep "(0):" | tail -1 | sed -e "s/^.*://; s/,//g")
    DIRECTION_OF_DETECTOR_Y_AXIS=$(h5dump -d "/entry/instrument/detector/module/slow_pixel_direction" $FIRSTFRAME 2>/dev/null | grep "(0):" | tail -1 | sed -e "s/^.*://; s/,//g")
    rotation_axis=$(h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g")
  else
    echo no NeXus header found.
   fi
   fi
  echo DATA_RANGE=$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 $2*1000}'`
Line 662: Line 734:
   #let SKIP=768
   #let SKIP=768
   #NX=$(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("'$FIRSTFRAME'","rb");f.seek(768);print "%.4d"%struct.unpack(">i",f.read(4))')
!  NY=$(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("'$FIRSTFRAME'","rb");f.seek(768);print("%.4d"%struct.unpack(">i",f.read(4)))')
   NX=$(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("'$FIRSTFRAME'","rb");f.seek(772);print("%.4d"%struct.unpack(">i",f.read(4)))')
!  DETECTOR_DISTANCE=$(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("'$FIRSTFRAME'","rb");f.seek(540);print "%.4f"%struct.unpack(">f",f.read(4))')
!  ORGY=$(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("'$FIRSTFRAME'","rb");f.seek(540);print("%.4f"%struct.unpack(">f",f.read(4)))')
   ORGX=$(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("'$FIRSTFRAME'","rb");f.seek(544);print("%.4f"%struct.unpack(">f",f.read(4)))')
!  OSCILLATION_RANGE=$(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("'$FIRSTFRAME'","rb");f.seek(776);print "%.6f"%struct.unpack(">f",f.read(4))')
!  QY=$(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("'$FIRSTFRAME'","rb");f.seek(776);print("%.6f"%struct.unpack(">f",f.read(4)))')
   QX=$(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("'$FIRSTFRAME'","rb");f.seek(780);print("%.6f"%struct.unpack(">f",f.read(4)))')
!  X_RAY_WAVELENGTH=$(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)))')


Line 933: Line 991:
! 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= $DETECTOR
Line 948: Line 1,005:
if [ "$DET" == "eiger" ] && [ "$is_h5" == 1 ]; then
if [ "$DET" == "eiger" ] && [ "$is_h5" == 1 ]; then
   if [ "$DLS" == 0 ] ; then
   if [ "$DLS" == 0 ] ; then
     if [ -e /usr/local/lib64/dectris-neggia.so ]; then
     neggia_path=/usr/local/lib64/dectris-neggia.so
       echo LIB=/usr/local/lib64/dectris-neggia.so >> XDS.INP
    if [ -e $neggia_path ]; then
       echo LIB= line was written to XDS.INP
       echo LIB=$neggia_path >> XDS.INP
       echo "LIB= <dectris-neggia> was written to XDS.INP . Check the path! For Apple M1 processors, 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
       echo /usr/local/lib64/dectris-neggia.so was not found - specify location manually!
       echo "dectris-neggia.so not found. Specify LIB=<path-to-dectris-neggia> in XDS.INP & fix your generate_XDS.INP !"
     fi
     fi
   else
   else
     if [ -e /usr/local/lib64/durin-plugin.so ]; then
     durin_path=/usr/local/lib64/durin-plugin.so
       echo LIB=/usr/local/lib64/durin-plugin.so >> XDS.INP
    if [ -e $durin_path ]; then
       echo LIB= line was written to XDS.INP
       echo LIB=$durin_path >> XDS.INP
       echo "LIB= <durin-plugin> was written to XDS.INP . Check the path! For Apple M1 processors, modify the name."
     else
     else
       echo !LIB=/usr/local/lib64/durin-plugin.so >> XDS.INP
       echo !LIB=/usr/local/lib64/durin-plugin.so >> XDS.INP
       echo /usr/local/lib64/durin-plugin.so was not found - specify location manually!
       echo "durin-plugin.so not found. Specify LIB=<path-to-durin-plugin> in XDS.INP & fix your generate_XDS.INP !"
     fi
     fi
   fi  
   fi  
Line 991: Line 1,050:
  cat >> XDS.INP << eof
  cat >> XDS.INP << eof
DIRECTION_OF_DETECTOR_X-AXIS=$DIRECTION_OF_DETECTOR_X_AXIS
DIRECTION_OF_DETECTOR_X-AXIS=$DIRECTION_OF_DETECTOR_X_AXIS
DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0
DIRECTION_OF_DETECTOR_Y-AXIS=$DIRECTION_OF_DETECTOR_Y_AXIS
eof
eof
  fi
  fi
Line 1,156: Line 1,215:
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, is at
echo Full documentation, including complete detector templates, at xds.mr.mpg.de .
echo http://www.mpimf-heidelberg.mpg.de/~kabsch/xds . More documentation in XDSwiki
echo More documentation in strucbio.biologie.uni-konstanz.de/xdswiki/index.php .
echo After running xds, inspect, using XDS-Viewer, at least the beamstop mask in
echo After running xds, inspect at least the agreement of predicted and observed  
echo BKGPIX.cbf, and the agreement of predicted and observed spots in FRAME.cbf!
echo spots in FRAME.cbf!
rm -f tmp1 tmp2
rm -f tmp1 tmp2
</pre>
</pre>


Line 1,167: Line 1,225:


Ask your system adminstrator to cut-and-paste the script into e.g. /usr/local/bin/generate_XDS.INP, and to make it "executable".
Ask your system adminstrator to cut-and-paste the script into e.g. /usr/local/bin/generate_XDS.INP, and to make it "executable".
If you work with Eiger data, you may want to make a one-line change to the script after downloading, in order to point to the correct path on your system of the Dectris' Neggia library, or the Durin plugin, respectively. Just open the script with an editor and adjust neggia_path or durin_path ! This relieves users from having to change the LIB= line for every data set. You should also insert that path into the Menu / Settings / "generic library" in [[XDSGUI]] .


But you may also cut-and-paste the script from this webpage into a file in e.g. your home directory; the filename should be generate_XDS.INP. After creating the file, make it executable - e.g. if it's in your $HOME, use:
But you may also cut-and-paste the script from this webpage into a file in e.g. your home directory; the filename should be generate_XDS.INP. After creating the file, make it executable - e.g. if it's in your $HOME, use:
Line 1,202: Line 1,262:
</pre>
</pre>
If you do use cut-and-paste from the webpage, be aware of the following problem report: On the Mac, after loading frames, by clicking “generate XDS.INP”, the program gives some strange symbol “” in XDS.INP. And the more you click “save” button, the more “” appear. This looks like e.g. <br>SPACE_GROUP_NUMBER=0  ! 0 if unknown <br>UNIT_CELL_CONSTANTS= 70 80 90 90 90 90  <br> ''The problem is due to the “Rich text” format in TextEdit when saving "generate_XDS.INP". It is solved by re-downloading the script, and changing format to Plain - everything should work then.''
If you do use cut-and-paste from the webpage, be aware of the following problem report: On the Mac, after loading frames, by clicking “generate XDS.INP”, the program gives some strange symbol “” in XDS.INP. And the more you click “save” button, the more “” appear. This looks like e.g. <br>SPACE_GROUP_NUMBER=0  ! 0 if unknown <br>UNIT_CELL_CONSTANTS= 70 80 90 90 90 90  <br> ''The problem is due to the “Rich text” format in TextEdit when saving "generate_XDS.INP". It is solved by re-downloading the script, and changing format to Plain - everything should work then.''
Attention beamline staff: it would be great if you could make a one-line change to the script after downloading, in order to point to the correct path to Dectris' Neggia library, or the Durin plugin, respectively. Just open the script with an editor and adjust neggia_path or durin_path ! This relieves users from having to change the LIB= line for every data set.


== Calling generate_XDS.INP from a Python script ==
== Calling generate_XDS.INP from a Python script ==
Line 1,244: Line 1,306:
* 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]].
* 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 .
* 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 always be determined 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 ==
Kay
Bureaucrats
2,652

edits

Retrieved from "https://wiki.uni-konstanz.de/xds/index.php/Special:MobileDiff/4320...4422"
Cookies help us deliver our services. By using our services, you agree to our use of cookies.
More information

Navigation menu