Difference between revisions of "Generate XDS.INP"

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Line 10: Line 10:
 
  ~/generate_XDS.INP "frms/mydata_1_???.img"
 
  ~/generate_XDS.INP "frms/mydata_1_???.img"
 
By using your own file, you can easily update to the latest revision, or even change the script, without having to bother the system administrator.
 
By using your own file, you can easily update to the latest revision, or even change the script, without having to bother the system administrator.
 +
 +
Instead of cut-and-paste, you could try
 +
wget http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP -O - | awk '/bash/,/rm -f tmp1 tmp2/' | \
 +
sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g > generate_XDS.INP
 +
to obtain generate_XDS.INP in your current directory.
  
 
This is the script:
 
This is the script:
Line 82: Line 87:
 
# and set a link if necessary
 
# and set a link if necessary
 
if [ ${#1} -gt 72 ]; then
 
if [ ${#1} -gt 72 ]; then
     TMP_PATH=$(/bin/ls -C1 $1 $1.bz2 | head -1)
+
     TMP_PATH=$(/bin/ls -C1 $1 $1.bz2 2>/dev/null | head -1)
 
     TMP_FILENAME=$(basename ${TMP_PATH})
 
     TMP_FILENAME=$(basename ${TMP_PATH})
 
     if [ ${#TMP_FILENAME} -gt 65 ]; then
 
     if [ ${#TMP_FILENAME} -gt 65 ]; then

Revision as of 21:57, 15 July 2011

This script generates XDS.INP based on a list of frame names supplied on the commandline.

Currently works for MarCCD, ADSC and Pilatus 6M detectors. Also supports bzip2-ed frames (when specifying the frame names, leave out the .bz2 extension, as documented for XDS!).

Installation: ask your system adminstrator to cut-and-paste it into e.g. /usr/local/bin/generate_XDS.INP , and to make it "executable". Usage is then just (don't forget the quotation marks!):

generate_XDS.INP "frms/mydata_1_???.img"

But you may also just cut-and-paste the script from this webpage into 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:

chmod +x ~/generate_XDS.INP

After that, you can just run it in the same way:

~/generate_XDS.INP "frms/mydata_1_???.img"

By using your own file, you can easily update to the latest revision, or even change the script, without having to bother the system administrator.

Instead of cut-and-paste, you could try

wget http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP -O - | awk '/bash/,/rm -f tmp1 tmp2/' | \
sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g > generate_XDS.INP

to obtain generate_XDS.INP in your current directory.

This is the script:

#!/bin/bash
# purpose: generate XDS.INP
#
# tested with some datasets from ALS, SSRL, SLS, ESRF and BESSY; only MARCCD, ADSC/SMV, PILATUS 6M detectors; 
# for other detectors, values marked with XXX must be manually filled in.
#
# revision 0.03 . Kay Diederichs 2/2010 
# revision 0.04 . Kay Diederichs 4/2010 - include alternative ORGX, ORGY calculations for ADSC
# revision 0.05 . Kay Diederichs 5/2010 - grep for "Corrected" in addition to "marccd"; needed for BESSY 
# revision 0.06 . KD 6/2010 - add UNTRUSTED_RECTANGLE and UNTRUSTED_ELLIPSE; use `whereis catmar` and so on 
# revision 0.07 . KD 6/2010 - decide about ORGX/Y info in MAR header being pixels or mm; other fixes
# revision 0.08 . KD 6/2010 - fixes for Pilatus 6M
# revision 0.09 . KD 6/2010 - get rid of requirement for mccd_xdsparams.pl and/or catmar; rather use "od"
# revision 0.10 . Tim Gruene 7/2010 - set link 'images' to image directory if path exceeds 72 characters
# revision 0.11 . KD 7/2010 - for MarCCD: look for distance info at different byte position
# revision 0.12 . KD 7/2010 - fix for negative PHISTART
# revision 0.13 . KD 8/2010 - store correct NX NY QX QY in XDS.INP
# revision 0.14 . KD 1/2011 - SENSOR_THICKNESS for Pilatus; MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3
# revision 0.15 . KD 2/2011 - add comment for -ive sign of APS 19-ID and Australian Synchrotron rotation axis
# revision 0.16 . KD 3/2011 - SENSOR_THICKNESS=0.01 for ADSC and MarCCD. Add comment about SILICON=
# revision 0.17 . KD 3/2011 - make it work for .bz2 frames; improve screen output
# revision 0.18 . KD 4/2011 - faster by doing "strings" only once; revert "images/${1##/*/}" "correction"
# revision 0.19 . KD 6/2011 - bugfix for 0.18
# revision 0.20 . KD 7/2011 - redirect stderr of /bin/ls to /dev/null
REVISION="0.20 (15-Jul-2011)"
#
# usage: e.g. generate_XDS.INP "frms/mydata_1_???.img"
# make sure to have the two quotation marks !
# the ? are wildcards for the frame numbers.
# 
# limitations:
# - frame numbers are assumed to start with 1 and run consecutively
# 
# known problems:
# - 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)
#
# 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 ======
echo generate_XDS.INP version $REVISION . Obtain the latest version from
echo http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP
if [ "$1" == "help" ] || [ "$1" == "-help" ] || [ "$1" == "-h" ]; then
  echo usage: generate_XDS.INP \"frms/mydata_1_???.img\"   \(_with_ the quotation marks!\)
  echo if the frames are compressed with bzip2, leave out the .bz2 extension!
  exit
fi
#
# defaults:
#
DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX"
ORGX=XXX
ORGY=XXX
DETECTOR_DISTANCE=XXX
OSCILLATION_RANGE=XXX
X_RAY_WAVELENGTH=XXX
QX=XXX
QY=XXX
NX=XXX
NY=XXX
SENSOR_THICKNESS=0
# see how we are called:
NAME_TEMPLATE_OF_DATA_FRAMES="$1"

# check that the image template name does not exceed 72 characters
# and set a link if necessary
if [ ${#1} -gt 72 ]; then
    TMP_PATH=$(/bin/ls -C1 $1 $1.bz2 2>/dev/null | head -1)
    TMP_FILENAME=$(basename ${TMP_PATH})
    if [ ${#TMP_FILENAME} -gt 65 ]; then
	echo "---> Unable to proceed: image filename "
	echo "--->  \"${TMP_FILENAME}\""
        echo "---> exceeds 72 characters."
        echo "---> Please rename files or set links."	
	exit
    else
	echo "---> Warning: Template name exceeds 72 characters. Setting link \"images\""
        echo "              to image directory"
	TMP_DIRNAME=$(dirname ${TMP_PATH})
	if [ -e "images" ]; then
	    echo "***  Error:   The file or directory \"images\" already exists. Please remove"
	    echo "              and re-run."
	    exit
	else
	    ln -s ${TMP_DIRNAME} images
	fi
	NAME_TEMPLATE_OF_DATA_FRAMES="images/${1##/*/}"
# KD 30.3.11 I believe the previous line should be changed to:
#      NAME_TEMPLATE_OF_DATA_FRAMES="images/${TMP_FILENAME}" 
# but I have not had the time to properly test this
	echo "              Using template filename \"${NAME_TEMPLATE_OF_DATA_FRAMES}\""
    fi
fi

# list frames matching the wildcards in NAME_TEMPLATE_OF_DATA_FRAMES
# don't accept the "direct beam" shot at SLS/Pilatus PX-I and PX-II
/bin/ls -C1 $1 $1.bz2 2>/dev/null | egrep -v "_00000.cbf|_000.img" > tmp1 || exit 1

# we can continue - the frames are found

# 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
FIRSTFRAME=`head -1 tmp1`
echo $FIRSTFRAME | grep -q bz2 && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1
strings $FIRSTFRAME > tmp2
egrep -q 'marccd|Corrected' tmp2 && DET=mccd
grep -q PILATUS tmp2             && DET=pilatus
grep -q BEAM_CENTER_X tmp2       && DET=adsc
# identify other detector types in the same way (MAR IP would be straightforward)

# parse ASCII header of first frame

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
  echo Data from a MarCCD detector
  
  DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500"
  SENSOR_THICKNESS=0.01
  # use first frame of dataset to obtain parameters

  # offsets are documented; values can be find in mccd_xdsparams.pl script
  let SKIP=1024+80
  NX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  let SKIP=$SKIP+4
  NY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')

  let SKIP=1720
  DETECTOR_DISTANCE=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  DETECTOR_DISTANCE=`echo "scale=3; $DETECTOR_DISTANCE/1000" | bc -l`
    
  let SKIP=1024+256+128+256+4
  ORGX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  ORGX=`echo "scale=2; $ORGX/1000" | bc -l `
  let SKIP=$SKIP+4
  ORGY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  ORGY=`echo "scale=2; $ORGY/1000" | bc -l `

  let SKIP=1024+256+128+256+44
  PHISTART=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  let SKIP=1024+256+128+256+76
  PHIEND=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  OSCILLATION_RANGE=`echo "scale=3; ($PHIEND-($PHISTART))/1000" | bc -l`
  
  let SKIP=1024+256+128+256+128+4
  QX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  QX=`echo "scale=10; $QX/1000000" |bc -l `
  let SKIP=$SKIP+4
  QY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  QY=`echo "scale=10; $QY/1000000" |bc -l `

  let SKIP=1024+256+128+256+128+128+12
  X_RAY_WAVELENGTH=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  X_RAY_WAVELENGTH=`echo "scale=5; $X_RAY_WAVELENGTH/100000" | bc -l`

# at most BLs, ORGX and ORGY are in pixels, but sometimes in mm ... guess:
  NXBYFOUR=`echo "scale=0; $NX/4" | bc -l `
  ORGXINT=`echo "scale=0; $ORGX/1" | bc -l `
  if [ $ORGXINT -lt $NXBYFOUR ]; then
     ORGX=`echo "scale=1; $ORGX/$QX" | bc -l`
     ORGY=`echo "scale=1; $ORGY/$QY" | bc -l`
     echo MARCCD detector: header ORGX, ORGY seem to be in mm ... converting to pixels
  else
     echo MARCCD detector: header ORGX, ORGY seem to be in pixel units
  fi

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:
  SENSOR_THICKNESS=0.01
  sed s/\;// tmp2 > tmp1
  mv tmp1 tmp2

      # find X_RAY_WAVELENGTH:
      X_RAY_WAVELENGTH=`grep WAVELENGTH tmp2 | head -1 | 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=//`
# FIXME - next 2 lines should be done properly, from header
      NY=$NX      
      QY=$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=//`
# fix 2010-04-26 - tell user about possible ORGX, ORGY alternatives -  
# at ESRF and ... (pls fill in!) the following should be used:
      ORGX=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l `
      ORGY=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l `
      echo - at ESRF BLs use: ORGX=$ORGX ORGY=$ORGY 
# this 2nd alternative convention should be used at the following beamlines (pls complete the list): ALS 5.0.3, ...
      ORGX=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l `
      ORGY=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l `
      echo - at e.g. ALS 5.0.3 use: ORGX=$ORGX ORGY=$ORGY 
# this 3rd alternative convention should be used at the following beamlines (pls complete the list): ALS 8.2.2, ... 
      ORGX=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l `
      ORGY=`echo "scale=1; $NX-$BEAM_CENTER_Y/$QX" | bc -l `
      echo - at e.g. ALS 8.2.2 use: ORGX=$ORGX ORGY=$ORGY - this is written to XDS.INP
# the latter alternative is written into the generated XDS.INP ! You have to correct this manually in XDS.INP, or adjust this script.
      # 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="PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= 1048576  !PILATUS 6M"
  SENSOR_THICKNESS=0.32
  NX=2463 NY=2527 QX=0.172 QY=0.172
  echo Data from a Pilatus detector
  sed s/#// tmp2 > tmp1
  mv tmp1 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 generate 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
! REFERENCE_DATA_SET=xxx/XDS_ASCII.HKL ! e.g. to ensure consistent indexing  
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
!
! exclude (mask) untrusted areas of detector, e.g. beamstop shadow :
! UNTRUSTED_RECTANGLE= 1800 1950 2100 2150 ! x-min x-max y-min y-max ! repeat
! UNTRUSTED_ELLIPSE= 2034 2070 1850 2240 ! x-min x-max y-min y-max ! if needed
!
! 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: only use strong reflections (default is 3)
MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3 ! default of 6 is sometimes too high
REFINE(INTEGRATE)=CELL BEAM ORIENTATION ! AXIS DISTANCE 

! parameters specifically for this detector and beamline:
DETECTOR= $DETECTOR
SENSOR_THICKNESS= $SENSOR_THICKNESS 
! 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=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, APS 19-ID, Australian Synchrotron 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. The file has only the most important keywords.
echo Full documentation, including complete detector templates, is at
echo http://www.mpimf-heidelberg.mpg.de/~kabsch/xds . More documentation in XDSwiki
echo After running xds, inspect, using XDS-Viewer, at least the beamstop mask in
echo BKGPIX.cbf, and the agreement of predicted and observed spots in FRAME.cbf!
rm -f tmp1 tmp2