Generate XDS.INP: Difference between revisions

XDS [http://strucbio.biologie.uni-konstanz.de/~dikay/XDS_html_doc/html_doc/xds_parameters.html#NAME_TEMPLATE_OF_DATA_FRAMES= supports] bzip2-ed frames. Thus, when specifying the frame name parameter of the script, you should leave out any .bz2 extension.

== The script ==

<pre>

# revision 0.15 . KD 2/2011 - add comment for -ive sign of APS 19-ID and Australian Synchrotron rotation axis

# revision 0.21 . KD 11/2011 - SEPMIN, CLUSTER_RADIUS hints; read NX NY from header (for Pilatus 2M)

# revision 0.22 . KD 12/2011 - Pilatus 2M UNTRUSTED_RECTANGLE lines, SENSOR_THICKNESS from header

# revision 0.35 . KD 6/2013 - reduce 7000 to 6000 for shadow detection; insert comment about *_RESOLUTION_RANGE lines

# revision 0.36 . KD 6/2013 - insert NUMBER_OF_PROFILE_GRID* lines for Pilatus (suggested by C.Vonrhein)

# revision 0.38 . KD 2/2014 - change defaults for REFINE(IDXREF) and REFINE(INTEGRATE) such that more stable results are obtained for difficult datasets

# revision 0.39 . Keitaro 4/2014 - automatically set ROTATION_AXIS=-1 0 0 for MX225HS at SPring-8 BL32XU.

# revision 0.46 . Keitaro 6/2014 automatically set ROTATION_AXIS=-1 0 0 for Mar225 at SPring-8 BL26B2.

# revision 0.47 . Keitaro 7/2014 more generic dTREK format support (Saturn and RAXIS)

# revision 0.49 . Nobuhisa 2/2015 add  detector serial number for AichiSR BL2S1 to beam center convention 1

# revision 0.50 . KD 03/2015 workaround for Mar-1 change of parameter name "DISTANCE" to "POSITION" in REFINE(*) keywords

# revision 0.57 . KD 12/2015 start to take care of vertical ROTATION_AXIS at Diamond I24 - for now only introduce comment

# revision 0.58 . Keitaro 01/2016 fix for dTREK image: take 'rotation axis' information from header

# revision 0.60 . KD 04/04/2016 ADSC detector SN=458 at APS 19-ID has reverse phi (https://zenodo.org/record/45756)

# revision 0.61 . Keitaro 10/04/2016 Add Eiger hdf5 support (may be incomplete; UNTRUSTED_RECTANGLE=s not set) NEED h5dump.

# revision 0.72 . KD 8/03/2017 fix nframes lookup in Eiger master file

# revision 0.73 . KD 18/05/2017 for Andrey Nascimento: add Pilatus 2M S/N 24-0109 with ROTATION_AXIS=-1 0 0

# - for ADSC detectors, there are at least three ways to obtain ORGX and ORGY values from the header (see below);

REVERSE_PHI="no"

# default MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT

# default DIRECTION_OF_DETECTOR_X-AXIS

DIRECTION_OF_DETECTOR_X_AXIS="1 0 0"

# default FRACTION_OF_POLARIZATION

pol_frac=0.98

test "${dname}" == "" && dname="."

NAME_TEMPLATE_OF_DATA_FRAMES="${dname}/${bname}"

# list frames matching the wildcards in NAME_TEMPLATE_OF_DATA_FRAMES

# cope with blanks in directory / file name

IFS=$'\n'

if [ ! -s tmp1 ]

then

  data_last=`cut -b $pos1-$pos2 tmp1 | tail -n1 | bc`

  DATA_RANGE="$data_first $data_last"

  # set SPOT_RANGE to first half of DATA_RANGE

  data_num=`wc -l tmp1 | awk '{print $1}'`

  data_half=`echo "if ($data_half<=1) 1;if ($data_half>1) $data_half" | bc -l`

  spot_last=`echo "scale=0; $data_first+$data_half-1" | bc -l`

FIRSTFRAME=`head -1 tmp1`

echo $FIRSTFRAME | grep "\.h5$" && is_h5=1 || is_h5=0

# find out detector type

echo $FIRSTFRAME | grep -q '\.bz2$' && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1

# for mac/linux compatibility. zcat foo.gz doesn't work on mac.

unset IFS

if [ "$is_h5" == 0 ]; then

  # TODO: whenever FIRSTFRAME is used below, it should be copied to tmp2 (using IFS as above), and tmp2 should be used instead

  # this was done for "mccd", but still has to be done for the "raxis" detector types

  head -n1 tmp2 | grep -q "^RAXIS" && DET=raxis

  head -n1 tmp2 | grep -q "^R-AXIS" && DET=raxis

  grep -q "^SOURCE_WAVELENGTH= *1" tmp2 && DET=dtrek

else

  h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME | grep -i Eiger > /dev/null && DET=eiger

fi

# parse ASCII header of first frame

if [ "$DET" == "XXX" ]; then

# find parameters of first frame

   echo Data from a MarCCD detector

   DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500"

   # Check detector serial number and recognize beamline for reversed-phi setting.

   # Known detectors for reversed-phi in SPring-8: 24: BL26B2 Mar225, 31: BL32XU MX225HE, 38: BL44XU MX225HE, 42: BL44XU MX300HE, 40: BL41XU MX225HE, 106: BL32XU MX225HS

   REVERSEPHI_SNs="

24

40

42

106

"

   if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then

     REVERSE_PHI="yes"

   fi

   cp $FIRSTFRAME tmp2

   unset IFS

   NX=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}')

   NY=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}')

   let SKIP=1720

   DETECTOR_DISTANCE=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}')

   let SKIP=1024+736

   let SKIP=1024+256+128+256+128+128+12

   X_RAY_WAVELENGTH=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}')

# at most BLs, ORGX and ORGY are in pixels, but sometimes in mm ... guess:

     echo MARCCD detector: header ORGX, ORGY seem to be in mm ... converting to pixels

elif [ "$DET" == "adsc" ]; then

   DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000"

   echo Data from ADSC detector. Obtaining ORGX, ORGY depends on beamline setup:

       # find X_RAY_WAVELENGTH:

       # find NX, QX, ORGX and ORGY:

       NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//`

       QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//`

       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=//`

       COMMENT_ORGXY="

! Following are possible beam center interpretations for ADSC detectors"

       ORGX1=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l`

       ORGY1=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l`

       COMMENT_ORGXY="${COMMENT_ORGXY}

# this 2nd alternative convention should be used at the following beamlines (pls complete the list): ALS 5.0.3, ...

       ORGX2=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l `

       ORGY2=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l `

       COMMENT_ORGXY="${COMMENT_ORGXY}

! ORGX= $ORGX2 ORGY= $ORGY2 ! For ALS 5.0.3,.."

# this alternative is written into the generated XDS.INP ! You have to correct this manually in XDS.INP, or adjust this script.

       ORGX3=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l `

       ORGX4=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l `

       ORGY4=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l `

       COMMENT_ORGXY="${COMMENT_ORGXY}

! ORGX= $ORGX4 ORGY= $ORGY4 ! For SPring-8,.."

       # Decision of beam center convention based on detector serial numbers.

       DET_SN=`grep DETECTOR_SN tmp2 | sed -e "s/DETECTOR_SN=//"`

       ORG1_SNs="

449

446

916

"

       ORG4_SNs="

       ORGX=$ORGX1

       ORGY=$ORGY1

       elif echo "${DET_SN}${ORG4_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then

       ORGX=$ORGX4

       ORGY=$ORGY4

       else

       ORGX=$ORGX3

       ORGY=$ORGY3

       fi

       # Check detector serial number and recognize beamline for reversed-phi setting.

       # Known detectors for reversed-phi in SPring-8: 915: BL38B1 Q315; APS 19-ID: 458; BM30A: 924

       REVERSEPHI_SNs="

915

924

"

       if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then

         REVERSE_PHI="yes"

       fi

elif [ "$DET" == "adsc-CMOS1" ]; then

   DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000"

   echo Data from CMOS1 MBC detector.

   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=//`

   ORGX=`grep BEAM_CENTER_X tmp2 | sed s/BEAM_CENTER_X=//`

   ORGY=`grep BEAM_CENTER_Y tmp2 | sed s/BEAM_CENTER_Y=//`

   REVERSE_PHI="yes"

elif [ "$DET" == "pilatus" ]; then

       # find SENSOR_THICKNESS:

       # find NX and NY; 2463/2527 is 6M, 1475/1679 is 2M

       NX=`grep X-Binary-Size-Fastest-Dimension tmp2 | awk '{print $2}'`

       # find ORGX and ORGY:

       ORGY=`grep Beam_xy tmp2 | sed -e s/\(// -e s/\)// -e s/\,// | awk '{print $3}'`

       DETECTOR_DISTANCE=`echo "$DETECTOR_DISTANCE*1000" | bc -l`

       # get detector serial number and check if it is included in the list

       # Known detectors for reversed-phi in APS: 19ID PILATUS3 6M 60-0132

       # Known detectors for reversed-phi at MX2 beamline (Brazilian Synchrotron National Laboratory - LNLS)

       DET_SN=`grep "Detector:" tmp2 | sed "s/^.*Detector: *//"`

       REVERSEPHI_SNs="

PILATUS3 6M, S/N 60-0125

PILATUS3 6M, S/N 60-0132

PILATUS 2M, S/N 24-0109

"

       if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then

         REVERSE_PHI="yes"

       fi

# Diamond I24:

       if [ "$DET_SN" == "PILATUS3 6M, S/N 60-0119" ] ; then

         if grep -q "Oscillation_axis X.CW +SLOW" tmp2 ; then

         fi

       fi

elif [ "$DET" == "eiger" ]; then

   QX=`h5dump -d "/entry/instrument/detector/x_pixel_size" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'`

   QY=`h5dump -d "/entry/instrument/detector/y_pixel_size" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'`

elif [ "$DET" == "raxis" ]; then

   DETECTOR="RAXIS MINIMUM_VALID_PIXEL_VALUE=0  OVERLOAD=2000000"

   #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)

elif [ "$DET" == "dtrek" ]; then

   dname=`grep "DETECTOR_NAMES=" tmp2 | sed -e "s/.*=//"`

   if [ "$dname" == "CCD_" ]; then

     DETECTOR="SATURN MINIMUM_VALID_PIXEL_VALUE=1"

     dtrek_det="saturn"

     echo ""

     echo "Please report this to XDSwiki author."

     echo ""

   fi

   # find OVERLOAD

   SATURATED_VALUE=`grep SATURATED_VALUE tmp2 | head -1 | sed s/SATURATED_VALUE=//`

   ORGY=${SPATIAL_DISTORTION_INFO[1]}

   GONIO_NAMES=(`grep ${dname}GONIO_NAMES= tmp2 | tail -1 | sed s/.*_GONIO_NAMES=//`)

   GONIO_VALUES=(`grep ${dname}GONIO_VALUES= tmp2 | tail -1 | sed s/.*_GONIO_VALUES=//`)

   idx=$((i-1))

   if [ "${GONIO_NAMES[$idx]}" == "Distance" ]; then

   fi

   done

   ROTATION=(`grep "^ROTATION=" tmp2 | tail -1 | sed s/ROTATION=//`)

   OSCILLATION_RANGE=${ROTATION[2]}

elif [ "$DET" == "MAR345" ]; then

  echo  "Data from a Mar345 image plate detector"

  DETECTOR="MAR345  MINIMUM_VALID_PIXEL_VALUE=0  OVERLOAD=130000"

  if grep -q 'CENTER' tmp2; then

   echo Beam center found.

   ORGY=`echo $NY / 2 | bc`

  fi

elif [ "$DET" == "Bruker-cbf" ]; then

  echo  "Data from a Bruker-cbf detector"

# MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT:

# use complete detector including corners:

# polarization

  pol_frac=`echo "${pol_frac}+0.5" | bc -l`

  DETECTOR="BRUKER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=${OVERLOAD}"

# ORGX/Y-offsets relative to center of detector:

  ORGY=`echo "scale=2; ${NY}/2-($ORGY/$QY)" | bc -l`

# test whether the absolute value of deltaphi is > absolute value of deltaomega

  if (( $(echo "${DELTAPHI}^2 > ${DELTAOMEGA}^2"|bc -l) )); then

     R1=`echo "scale=7; s($KAPPA/$DEGTOR)*c($OMEGA/$DEGTOR)" | bc -l`

     R2=`echo "scale=7; c($KAPPA/$DEGTOR)          " | bc -l`

     OSCILLATION_RANGE=${DELTAPHI}

  else

     echo OMEGA scan

     OSCILLATION_RANGE=${DELTAOMEGA}

  fi

# 2theta

   echo TWOTHETA=$TWOTHETA

   R1=`echo "scale=7; c($TWOTHETA/$DEGTOR)" | bc -l`

else

   echo should never come here

cat > XDS.INP << eof

! written by generate_XDS.INP version $REVISION

JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT

$COMMENT_ORGXY

NAME_TEMPLATE_OF_DATA_FRAMES=$NAME_TEMPLATE_OF_DATA_FRAMES

SPACE_GROUP_NUMBER=0                  ! 0 if unknown

STRONG_PIXEL=4          ! COLSPOT: only use strong reflections (default is 3)

MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=$MNOPIAS ! default of 6 is sometimes too high

! parameters specifically for this detector and beamline:

DETECTOR= $DETECTOR

! attention CCD detectors: for very high resolution (better than 1A) make sure to specify SILICON

! as about 32* what CORRECT.LP suggests (absorption of phosphor is much higher than that of silicon).

NX= $NX NY= $NY  QX= $QX  QY= $QY ! to make CORRECT happy if frames are unavailable

DIRECTION_OF_DETECTOR_X-AXIS=$DIRECTION_OF_DETECTOR_X_AXIS

eof

cat >> XDS.INP << eof

!used by DEFPIX and CORRECT to exclude ice-reflections / ice rings - uncomment if necessary

!EXCLUDE_RESOLUTION_RANGE= 3.93 3.87 !ice-ring at 3.897 Angstrom

!EXCLUDE_RESOLUTION_RANGE= 3.70 3.64 !ice-ring at 3.669 Angstrom

eof

if [ "$DET" == "Bruker-cbf" ]; then

   echo "DELPHI=15 ! refine less often than the default of 5" >> XDS.INP

elif [ "$DET" == "adsc-CMOS1" ]; then

   echo UNTRUSTED_RECTANGLE= 0 1468  2451 2631  >> XDS.INP

elif [ "$DET" == "pilatus" -o "$DET" == "eiger" ]; then

cat >> XDS.INP << eof

eof

     if ! grep -q Flat_field tmp2 ; then

     cat >> XDS.INP << eof

! the following specifications are for a detector _without_ proper

! to each UNTRUSTED_RECTANGLE

!EXCLUSION OF VERTICAL DEAD AREAS OF THE PILATUS 2M DETECTOR

eof

     fi

# Pilatus 6M

# FIXME: here we could test if a Flat_field correction was applied like we do for 2M

UNTRUSTED_RECTANGLE=  0 2464  2315 2333

eof

# Eiger 9M

     cat >> XDS.INP << eof

UNTRUSTED_RECTANGLE= 0 3110 2717 2757

eof

# Eiger 16M

     cat >> XDS.INP << eof

!EXCLUSION OF VERTICAL DEAD AREAS OF THE EIGER 16M DETECTOR + ONE PIXEL ON EACH SIDE

  UNTRUSTED_RECTANGLE= 1029 1042      0 4371

  UNTRUSTED_RECTANGLE= 3109 3122      0 4371

eof

   fi