Generate XDS.INP

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Revision as of 16:17, 24 February 2010 by Kay (talk | contribs) (New page: This script should be in your $PATH as "generate_XDS.INP" #!/bin/bash # purpose: generate XDS.INP # revision 0.03 . Kay Diederichs 2/2010 # tested with own and some JCSG datasets; ...)
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This script should be in your $PATH as "generate_XDS.INP"

#!/bin/bash

# purpose: generate XDS.INP
# revision 0.03 . Kay Diederichs 2/2010 
# tested with own and some JCSG datasets; only MARCCD, ADSC/SMV, PILATUS detectors; for other detectors, values must be manually filled in.
#
# usage: e.g. generate_XDS.INP.rc "frms/mydata_1_???.img"
# make sure to have the two "  !
# the ? are wildcards for the frame numbers.
#
# requirement for external programs(s):
# - for MARCCD detectors the "catmar" binary (which can be downloaded from http://www.marresearch.com/download.html) must be in $PATH
# - alternatively, the mccd_xdsparams.pl script (see http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Mccd_xdsparams.pl ) will be used, courtesy of Ana Gonzalez.
# 
# limitations:
# - frame numbers are assumed to start with 1 and run consecutively
# 
# known problems:
# - for ADSC detectors, the ORGX and ORGY values are inaccurate; the "imgheader" program that I have delivers better values, but I don't know how and why.
#
# notes for debugging of the script:
# - add the -v option to the first line, to see where an error occurs
# - comment out the removal of tmp1 and tmp2 in the last line
#
# ====== Start of script ======
#
# defaults:
#

DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX"
ORGX=XXX
ORGY=XXX
DETECTOR_DISTANCE=XXX
OSCILLATION_RANGE=XXX
X_RAY_WAVELENGTH=XXX

# see how we are called:
NAME_TEMPLATE_OF_DATA_FRAMES="$1"

# list frames matching the wildcards in NAME_TEMPLATE_OF_DATA_FRAMES
ls -C1 $1 > tmp1

# set upper limit of DATA_RANGE to number of frames (see "limitations" above)
DATA_RANGE=`wc -l tmp1 | awk '{print $1}'`

# set upper limit of SPOT_RANGE to half of DATA_RANGE, but not less than 1
SPOT_RANGE=`echo "scale=0; $DATA_RANGE/2" | bc -l`
SPOT_RANGE=`echo "if ($SPOT_RANGE<1) 1;if ($SPOT_RANGE>1) $SPOT_RANGE" | bc -l`

echo DATA_RANGE=1 $DATA_RANGE

# find out detector type
DET=XXX
strings `head -1 tmp1` | grep -q marccd        && DET=mccd
strings `head -1 tmp1` | grep -q PILATUS       && DET=pilatus
strings `head -1 tmp1` | grep -q BEAM_CENTER_X && DET=adsc
# identify other detector types in the same way (MAR IP would be straightforward)

# parse ASCII header of first frame (except for MARCCD, which therefore requires catmar)

if [ "$DET" == "XXX" ]; then
  echo "this is not a MAR, ADSC/SMV or PILATUS detector - fill in XXX values manually!"
  DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX"

# find parameters of first frame
elif [ "$DET" == "mccd" ]; then

  DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000"
  echo this a a MARCCD detector
  if [ -e /usr/local/bin/catmar ]; then

      # inspect frame header and get rid of blanks in imgheader output:
      catmar `head -1 tmp1` | sed s/\ //g > tmp2

      # find X_RAY_WAVELENGTH:
      X_RAY_WAVELENGTH=`grep Wavelength tmp2 | sed s/Wavelength.Ang]=//`

      # find QX, ORGX and ORGY:
      QX=`grep Pixelsizex tmp2 | sed s/Pixelsizex=//`
      NX=`grep pixelsin1line tmp2 | sed s/#pixelsin1line=//`

      ORGX=`grep Centerx tmp2 | sed s/Centerx=//`
      ORGX=`echo "scale=1; ($ORGX+50)/1000" | bc -l `

      ORGY=`grep Centery tmp2 | sed s/Centery=//`
      ORGY=`echo "scale=1; ($ORGY+50)/1000" | bc -l `

      # find DETECTOR_DISTANCE and OSCILLATION_RANGE:
      DETECTOR_DISTANCE=`grep Distance tmp2 | sed s/Distance.mm]=//`
      STARTING_PHI=`grep StartingPHI tmp2 | sed s/StartingPHI=//`
      ENDING_PHI=`grep EndingPHI tmp2 | sed s/EndingPHI=//`
      OSCILLATION_RANGE=`echo "scale=3; ($ENDING_PHI-$STARTING_PHI)/1000" | bc -l`

  else
      if [ -e /usr/local/bin/mccd_xdsparams.pl ]; then
        mccd_xdsparams.pl -v `head -1 tmp1` > tmp2
        X_RAY_WAVELENGTH=`awk '/X-RAY_WAVELENGTH/{print $2}' tmp2`
        DETECTOR_DISTANCE=`awk '/DETECTOR_DISTANCE/{print $2}' tmp2`
        ORGX=`awk '/ORGX/{print $2}' tmp2`
        ORGY=`awk '/ORGY/{print $4}' tmp2`
        OSCILLATION_RANGE=`awk '/OSCILLATION_RANGE/{print $2}' tmp2`
      else
        echo "could not find /usr/local/bin/catmar - fill XXX values manually!"
      fi
  fi

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

  DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000"
  echo this is an ADSC detector
  strings `head -1 tmp1` | sed s/\;// > tmp2

      # find X_RAY_WAVELENGTH:
      X_RAY_WAVELENGTH=`grep WAVELENGTH tmp2 | sed s/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=//`
      ORGX=`grep BEAM_CENTER_X tmp2 | sed s/BEAM_CENTER_X=//`
      ORGX=`echo "scale=1; $ORGX/$QX" | bc -l `
      ORGY=`grep BEAM_CENTER_Y tmp2 | sed s/BEAM_CENTER_Y=//`
      ORGY=`echo "scale=1; $NX-$ORGY/$QX" | bc -l `

      # find DETECTOR_DISTANCE and OSCILLATION_RANGE:
      DETECTOR_DISTANCE=`grep DISTANCE tmp2 | sed s/DISTANCE=//`
      OSCILLATION_RANGE=`grep OSC_RANGE tmp2 | sed s/OSC_RANGE=//`

elif [ "$DET" == "pilatus" ]; then
  DETECTOR="DETECTOR=PILATUS  MINIMUM_VALID_PIXEL_VALUE=0  OVERLOAD= 1048576"
  echo this is a Pilatus detector
  head -50 `head -1 tmp1` | sed s/#//> tmp2

      # find X_RAY_WAVELENGTH:
      X_RAY_WAVELENGTH=`grep Wavelength tmp2 | sed -e s/Wavelength// -e s/A// | awk '{print $1}'`

      # find ORGX and ORGY:
      ORGX=`grep Beam_xy tmp2 | sed -e s/\(// -e s/\)// -e s/\,// | awk '{print $2}'`
      ORGY=`grep Beam_xy tmp2 | sed -e s/\(// -e s/\)// -e s/\,// | awk '{print $3}'`

      # find DETECTOR_DISTANCE and OSCILLATION_RANGE:
      DETECTOR_DISTANCE=`awk '/distance/{print $2}' tmp2`
      DETECTOR_DISTANCE=`echo "$DETECTOR_DISTANCE*1000" | bc -l`

      OSCILLATION_RANGE=`awk '/Angle/{print $2}' tmp2`

else
  echo should never come here
  exit 1
fi

echo ORGX= $ORGX ORGY= $ORGY - check these values with adxv !
echo DETECTOR_DISTANCE= $DETECTOR_DISTANCE
echo OSCILLATION_RANGE= $OSCILLATION_RANGE
echo X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH

# now we know everything that is required to write XDS.INP

cat >XDS.INP<<eof
JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
ORGX= $ORGX ORGY= $ORGY  ! check these values with adxv !
DETECTOR_DISTANCE= $DETECTOR_DISTANCE
OSCILLATION_RANGE= $OSCILLATION_RANGE
X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH
NAME_TEMPLATE_OF_DATA_FRAMES=$NAME_TEMPLATE_OF_DATA_FRAMES
DATA_RANGE=1 $DATA_RANGE
SPOT_RANGE=1 $SPOT_RANGE
# BACKGROUND_RANGE=1 10 ! rather use defaults (first 5 degree of rotation)

SPACE_GROUP_NUMBER=0                   ! 0 if unknown
UNIT_CELL_CONSTANTS= 70 80 90 90 90 90 ! put correct values if known
INCLUDE_RESOLUTION_RANGE=50 0  ! after CORRECT, insert high resol limit; re-run CORRECT


FRIEDEL'S_LAW=FALSE     ! This acts only on the CORRECT step
! If the anom signal turns out to be, or is known to be, very low or absent,
! use FRIEDEL'S_LAW=TRUE instead (or comment out the line); re-run CORRECT

! remove the "!" in the following line:
! STRICT_ABSORPTION_CORRECTION=TRUE
! if the anomalous signal is strong: in that case, in CORRECT.LP the three
! "CHI^2-VALUE OF FIT OF CORRECTION FACTORS" values are significantly> 1, e.g. 1.5

! parameters with changes wrt default values:
TRUSTED_REGION=0.00 1.2  ! partially use corners of detectors; 1.41421=full use
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=7000. 30000. ! often 8000 is ok
MINIMUM_ZETA=0.05        ! integrate close to the Lorentz zone; 0.15 is default
STRONG_PIXEL=6           ! COLSPOT: don't find weak reflections; default is 3
REFINE(INTEGRATE)=CELL BEAM ORIENTATION

! parameters specifically for this detector and beamline:
DETECTOR= $DETECTOR
!NX= 3072 NY= 3072  QX= 0.10260  QY= 0.10260 ! XDS finds this out by itself
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0
DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0
INCIDENT_BEAM_DIRECTION=0 0 1
ROTATION_AXIS=1 0 0    ! at e.g. SERCAT ID-22 this needs to be -1 0 0
FRACTION_OF_POLARIZATION=0.98   ! better value is provided by beamline staff!
POLARIZATION_PLANE_NORMAL=0 1 0
eof

echo "XDS.INP is ready for use."
echo "After running xds, inspect BKGPIX.cbf and FRAME.cbf with XDS-Viewer!"
# rm tmp1 tmp2