Generate XDS.INP
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This script generates XDS.INP based on a list of frame names supplied on the commandline. It currently works for MarCCD, ADSC and Pilatus detectors; since this is just a bash script, extension to other detectors is very easy.
On Mac OS X, installation of the "Command Line Tools" (from http://developer.apple.com/downloads; requires Apple ID) is required (I think). These are a part of the (larger, but also free) Xcode package.
Usage
Usage is just (don't forget the quotation marks!):
generate_XDS.INP "frms/mydata_1_???.img"
XDS supports bzip2-ed frames. Thus, when specifying the frame name parameter of the script, you should leave out any .bz2 extension.
The script
#!/bin/bash
# purpose: generate XDS.INP
#
# tested with some datasets from ALS, SSRL, SLS, ESRF and BESSY; only MARCCD, ADSC/SMV, PILATUS 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 0.21 . 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 0.23 . KD 1/2012 - add UNTRUSTED_QUADRILATERAL, remove MINIMUM_ZETA (0.05 is default now)
# revision 0.24 . KD 3/2012 - remove revision 0.10 since XDS now takes much longer paths
# revision 0.25 . KD 3/2012 - remove revision 0.22 for PSI Pilatus 2M; see http://www.globalphasing.com/autoproc/wiki/index.cgi?TroubleShootingKnownIssues
# revision 0.26 . KD 7/2012 - Mac-compatibility: replace od flags --skip-bytes= and --read-bytes= with -j and -N (thanks to Oliver Clarke for working this out!)
REVISION="0.26 (02-Jul-2012)"
#
# 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)
# - on Mac OS X, Xcode (from http://developer.apple.com/tools/xcode) might be needed - 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"
# 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 [ "$DET" == "mccd" ]; then
echo Data from a MarCCD detector
DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500"
SENSOR_THICKNESS=0.01
# use first frame of dataset to obtain parameters
# offsets are documented; values can be found in mccd_xdsparams.pl script
let SKIP=1024+80
NX=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
let SKIP=$SKIP+4
NY=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
let SKIP=1720
DETECTOR_DISTANCE=$(od -t dI -j $SKIP -N 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 -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
ORGX=`echo "scale=2; $ORGX/1000" | bc -l `
let SKIP=$SKIP+4
ORGY=$(od -t dI -j $SKIP -N 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 -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
let SKIP=1024+256+128+256+76
PHIEND=$(od -t dI -j $SKIP -N 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 -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
QX=`echo "scale=10; $QX/1000000" |bc -l `
let SKIP=$SKIP+4
QY=$(od -t dI -j $SKIP -N 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 -j $SKIP -N 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"
QX=0.172 QY=0.172
echo Data from a Pilatus detector
sed s/#// tmp2 > tmp1
mv tmp1 tmp2
# find SENSOR_THICKNESS:
SENSOR_THICKNESS=`grep thickness tmp2 | sed -e s/'Silicon sensor, thickness'// | awk '{print $1*1000}'`
# find X_RAY_WAVELENGTH:
X_RAY_WAVELENGTH=`grep Wavelength tmp2 | sed -e s/Wavelength// -e s/A// | awk '{print $1}'`
# find NX and NY; 2463/2527 is 6M, 1475/1679 is 2M
NX=`grep X-Binary-Size-Fastest-Dimension tmp2 | awk '{print $2}'`
NY=`grep X-Binary-Size-Second-Dimension tmp2 | awk '{print $2}'`
# 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
! written by generate_XDS.INP version $REVISION
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
! UNTRUSTED_QUADRILATERAL= x1 y1 x2 y2 x3 y3 x4 y4 ! see documentation
!
! 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
STRONG_PIXEL=4 ! COLSPOT: only use strong reflections (default is 3)
MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3 ! default of 6 is sometimes too high
! close spots: reduce SEPMIN and CLUSTER_RADIUS from their defaults of 6 and 3, e.g. to 4 and 2
! for bad or low resolution data remove the "!" in the following line:
! REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS ! DISTANCE
REFINE(INTEGRATE)=CELL BEAM ORIENTATION ! AXIS DISTANCE
! REFINE(CORRECT)=CELL BEAM ORIENTATION AXIS DISTANCE ! Default is: refine everything
! 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= $QY ! to make CORRECT happy if frames are unavailable
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0
DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0
INCIDENT_BEAM_DIRECTION=0 0 1
ROTATION_AXIS=1 0 0 ! at e.g. Australian Synchrotron, SERCAT ID-22 (?), APS 19-ID (?) this needs to be -1 0 0
FRACTION_OF_POLARIZATION=0.98 ! better value is provided by beamline staff!
POLARIZATION_PLANE_NORMAL=0 1 0
eof
if [ "$DET" == "pilatus" ]; then
if [ $NX == "1475" ]; then
if ! grep -q FF_p2m0109_E12398_T6199_vrf_m0p20.tif tmp2 ; then
cat >> XDS.INP << eof
!EXCLUSION OF VERTICAL DEAD AREAS OF THE PILATUS 2M DETECTOR
UNTRUSTED_RECTANGLE= 486 496 0 1680
UNTRUSTED_RECTANGLE= 980 990 0 1680
!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE PILATUS 2M DETECTOR
UNTRUSTED_RECTANGLE= 0 1476 194 214
UNTRUSTED_RECTANGLE= 0 1476 406 426
UNTRUSTED_RECTANGLE= 0 1476 618 638
UNTRUSTED_RECTANGLE= 0 1476 830 850
UNTRUSTED_RECTANGLE= 0 1476 1042 1062
UNTRUSTED_RECTANGLE= 0 1476 1254 1274
UNTRUSTED_RECTANGLE= 0 1476 1466 1486
eof
fi
# elif [ $NX == "2463" ]; then
# cat >> XDS.INP << eof
#eof
fi
fi
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
System-wide or personal installation
Ask your system adminstrator to cut-and-paste the script into e.g. /usr/local/bin/generate_XDS.INP, and to make it "executable".
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:
chmod +x ~/generate_XDS.INP
After that, you can just run it in the same way as if it were installed in your $PATH:
~/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.
Generating generate_XDS.INP from this webpage
Instead of cutting-and-pasting the lines of the script, you (or the system administrator) could just cut-and-paste the following four lines
wget http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP -O - | \ sed -e s/\ \;/\ /g -e s/\>\;/\>/g -e s/\<\;/\</g -e s/amp\;//g -e s/\"\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \ awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP chmod +x generate_XDS.INP
to copy the script from this website into an executable file generate_XDS.INP in your current directory.