Release notes
Version January 10, 2014
-
Adaptation to read Rigaku's modified image format (SMV) for 200/300K pixel
detectors
-
Correction of a bug in the determination of reference profiles in the
INTEGRATE step of XDS that could cause a program crash.
-
Correction of a bug in background determination in the INIT
step that could result in the (wrong) error message
'SPECIFIED DATA IMAGES UNAVAILABLE'
-
Increase from 8 to 9 positions for printing Rmeas in CORRECT.LP and XSCALE.LP.
This simplifies parsing the output by other programs.
-
Input file names up to 120 characters are now accepted by XSCALE
Version November 11, 2013
-
A possibility for omitting specified reflections from file INTEGRATE.HKL
in the CORRECT step has been included. These reflections are collected
in the new file
FILTER.HKL
Typically, the file is generated by a dedicated user program to handle
special experimental situations in which parts of the detector
become obscured.
-
Bug correction in the XYCORR step of XDS in the case of
a multi-segment detector at vanishing
DETECTOR_DISTANCE.
(Bug reported by Claus Flensburg.)
-
Correction of a bug in IDXREF that sometimes caused a failure to
recognize a given unit cell basis due to insufficient sampling of
possible basis orientations.
Version March 30, 2013
Version September 26, 2012
-
Bug correction in the IDXREF and CORRECT step of XDS. In some cases
basis vectors specified by the user in XDS.INP were ignored, using
non-equivalent alternative settings instead. The bug was introduced
in the previous version July 4, 2012 while earlier versions were o.k.
(bug reported by Clemens Vonrhein).
Version July 4, 2012
-
The four user input parameters REFLECTING_RANGE=, REFLECTING_RANGE_E.S.D.=,
BEAM_DIVERGENCE=, and BEAM_DIVERGENCE_E.S.D.= can be independently fixed
or automatically determined by XDS.
-
The new parameter, DATA_RANGE_FIXED_SCALE_FACTOR= i1 i2 s, was introduced
to allow an explicit specification of a scale factor 's' for each image
in the data range 'i1' to 'i2'. Any number of such parameters can be
specified. This new parameter replaces the previous one
FIXED_SCALE_FACTOR= TRUE
-
Removal of outliers from the comparison of the new data with a reference
data set in the CORRECT step. The outliers have sometimes caused low
correlation factors being reported.
Version March 15, 2012
-
Replacement of Rmrgd-F by a correlation factor CC(1/2) between random
half-datasets for reporting results in CORRECT and XSCALE. CC(1/2) is
a useful indicator of crystallographic information in each resolution
shell. (Karplus & Diederichs).
-
Correction of a bug in the INTEGRATE step that lead to small inaccuracies
in the percentage of observed reflection intensities (item PEAK in
INTEGRATE.HKL).
Version March 5, 2012
-
Correction of a bug in the INTEGRATE step that sometimes caused a
reading error (reported by Michel Fodje, Canadian Light Source).
-
Correction of a bug in the INTEGRATE step that lead to inaccurate
spot boundaries for rotation images with a large oscillation range.
(pinpointed by Kay Diederichs).
Version January 19, 2012
-
The input parameter
UNTRUSTED_QUADRILATERAL=
has been introduced to simplify exclusion of shaded pixel regions that
cannot be enclosed by border lines parallel to the detector's X and Y
directions.
-
The input parameter
MINIMUM_FRACTION_OF_BACKGROUND_REGION=
controls the minimum allowed size of background islands on the detector.
Version December 31, 2011
-
Improvements in the INTEGRATE step by modelling of individual reflection
routes through the Ewald sphere (mainly affecting spots close to the
rotation axis).
-
Improvements in the success rate of the IDXREF step.
-
Routines for processing BRUKER SMART6000 images have been reactivated.
(Note, that XDS cannot correct these images for spatial distortions!)
-
The input parameter
FIXED_SCALE_FACTOR=
has been introduced to handle data images with extremely low background.
Nearly vanishing background such as obtained from extremely fined-sliced
data from the PILATUS detector could lead to underestimated errors of the
integrated intensities. The optimal oscillation range need not be less
than half the crystal's mosaicity.
-
The input parameter
WFAC1=
is now provided also to XSCALE allowing the user additional control
on accepting symmetry related reflections for determination of correction
factors.
Version December 6, 2010
-
The new input parameter
SECONDS=
was introduced to check for the existence of a data image in units of
seconds rather than minutes. This new parameter
replaces the old parameter MINUTE= which is no longer accepted.
-
For stopping a running xds job more gracefully than by issuing CTRL-C
the user could now create a file named 'stop' in the XDS processing directory
by the command 'touch stop'. Each of the parallel threads then refuses to
process any more data images.
-
Correction of an error that prevented the reading of CBF-type files that are
compressed by gzip, bzip2, compress.
-
IDXREF now works more robustly with few reflections,
e.g. when indexing a single image.
-
Improvements in decision making for resolving ambiguities in the unit cell
basis vectors if a reference data set is present. (Effects CORRECT and XSCALE)
-
The recently developed fast scaling method
(Kabsch, 2010b)
was extended and is now again using the
smooth scaling equations (Kabsch, 1988b),
generally improving data quality.
Version May 10, 2010
-
Reduction of fluctuations in scaling factors of adjacent images with a
very low background (contributed by Kay Diederichs).
-
The new input parameter
UNTRUSTED_ELLIPSE=
was introduced to simplify exclusion of detector pixels behind the beam stop.
-
The highest signal-to-noise value that can be obtained by the experimental
set-up is reported in the CORRECT step as indicator of instrument error.
Version February 3, 2010
Version December 28, 2009
-
Error correction in determination of very low background for the PILATUS pixel
detector.
Version January 30, 2009
-
Automatic recognition of image file formats for most detectors currently in use.
-
XDS now uses 32 bit integers throughout to code image pixel values.
Control images generated by XDS are efficiently saved as 32 bit-pixels in the
CBF format, a byte-offset variant of the
CBFlib
format. Such images are indicated by the file name extension ".cbf".
-
The graphics program VIEW is no longer distributed with the XDS package.
It is recommended to use the open source program XDS-Viewer that
can display CBF-formatted images. Other file formats are supported
through the external conversion program 2cbf that comes with the XDS package.
XDS-Viewer is distributed under the GNU General Public License and must be
downloaded separately.
-
Executables of the XDS package for SGI (IRIX), Compaq alpha (Tru64), and
Apple Power Mac G4/G5 (OSX) are no longer provided.
Version September 10, 2008
-
Error correction in the CORRECT step of XDS. The error could prevent
the automatic selection of the correct unit cell setting with respect
to that of an external reference data set.
Version July 21, 2008
-
XDS now accepts images from the Rigaku Saturn 944+ CCD detector.
Version June 2, 2008
-
A subroutine to support space group determination was added to the
CORRECT step. Automatic assignments are based on a few decision
constants that can be modified by the user in XDS.INP. These new
input parameters are called
MAX_CELL_AXIS_ERROR=,
MAX_CELL_ANGLE_ERROR=,
TEST_RESOLUTION_RANGE=,
MIN_RFL_Rmeas=,
MAX_FAC_Rmeas=.
-
Bug correction in XDS. Error in calculating reflection boundaries for centered
lattices that could lead to inferior results at high resolution in the
INTEGRATE step (pointed out by Kay Diederichs).
Version December 6, 2007
-
Three new input parameters for use in the IDXREF step,
UNIT_CELL_A-AXIS=,
UNIT_CELL_B-AXIS=,
UNIT_CELL_C-AXIS=
have been introduced to help the user maintaining a consistent indexing
scheme between several data sets taken from the same crystal in the same
orientation.
-
The weighting scheme for obtaining reference profiles in the INTEGRATE
step that was introduced in the previous version proved inadequate
for data from the PILATUS pixel detector and has now been replaced by
the old weighting scheme.
-
Bug correction in XDS. The input parameter DATA_RANGE= was ignored in the
CORRECT step.
-
Bug correction in XSCALE. The column OBSERVED reported a too small number
of observed reflections in each resolution shell.
Version November 10, 2007
-
Minor change in weighting 3D reflection profiles in the determination
of references used for profile fitting in the INTEGRATE step. This may
result in a slight improvement of the final intensity data.
-
Small modification in estimating errors of reflection intensities resulting
in a reduction of random fluctuations of the errors.
Version October 10, 2007
-
Changes in the INTEGRATE step of XDS to reduce memory requirements. This
solves a problem in processing fine-sliced data images.
Version August 15, 2007
-
Minor bug corrections and simplifications in the use of XDSCONV and XSCALE.
Some of the input parameters, such as space group and cell constants, are
now extracted from the header of the input file by default. Note that the
definitions of the parameters
INPUT_FILE= and
OUTPUT_FILE= have
changed and a new parameter
INCLUDE_RESOLUTION_RANGE=
has been included in XDSCONV and XSCALE. Thus, files XSCALE.INP and XDSCONV.INP
that worked for the previous versions of the programs are likely to need a
modification.
Version July 5, 2007
-
Bug correction in CORRECT. The intervals for reporting the statistics
MEAN INTENSITY AS FUNCTION OF SPINDLE POSITION WITHIN DATA IMAGE
were incorrectly chosen.
-
Bug corrections in XDSCONV that affected the conversion to CCP4 format.
XDSCONV has been extensively revised and now uses the keywords
CCP4_F and
CCP4_I
instead of the old specifier FALL and IALL, respectively.
Version June 12, 2007
-
Improvements in CORRECT and XSCALE in calculations of correction factors
and error model parameters of reflection intensities.
Version May 8, 2007
-
The default value of the input parameter
STRICT_ABSORPTION_CORRECTION=
has been changed from TRUE to FALSE.
-
Minor changes in CORRECT and XSCALE in calculations of correction factors
and error model parameters of reflection intensities.
Version March 15, 2007
-
XDS now accepts images in the
CBFlib
format (new format keyword is CBF).
-
The new input parameters
SENSOR_THICKNESS=
SILICON=
were introduced to XDS to specify the finite thickness of the silicon
sensor of the PILATUS pixel detector. They are used in the XYCORR and
CORRECT steps to account for parallax- and sensitivity effects.
-
The old input parameter AIR=
has become optional as the appropriate, wavelength-dependent value
will be calculated by XDS.
-
The old input parameter MINPK=
is effective now in the INTEGRATE as well as in the CORRECT step.
-
Restrictions on the total number of parameters of types
UNTRUSTED_RECTANGLE=,
SPOT_RANGE=, and
EXCLUDE_RESOLUTION_RANGE=
have been removed.
-
A new input parameter
CORRECTIONS=
has been introduced to allow the user to specify which corrections
should be made in CORRECT/XSCALE
Version December 6, 2006
-
New routines in CORRECT and XSCALE for rapid calculation of data correction
factors. The correction factors are provided as color coded 2-D images that
can be inspected with the VIEW program of the XDS-package.
-
Improved diagostics in CORRECT and XSCALE for detecting anomalous
signals in the collected data.
-
The new input parameter
MINIMUM_I/SIGMA=
was introduced to XDS and XSCALE which defines the minimum signal-to-noise
for reflections included in correction/scaling factor determinations.
-
The new input parameter
REFLECTIONS/CORRECTION_FACTOR=
was introduced to XDS and XSCALE which defines the minimum number
of reflections needed for the determination of each correction factor.
-
The new input parameter
MINIMUM_ZETA=
allows the user to specify the size of the 'blind region' for
excluding reflections close to the rotation axis.
Version August 18, 2006
-
Correction of an old bug in IDXREF. In rare cases this bug could
prevent the interpretation of the observed reduced cell vectors in
terms of the conventional cell leading to failure of IDXREF.
-
Correction of a bug in CORRECT introduced in the August 8 release. This
bug could lead to a core dump if an external reference data set was used.
-
First release of XDS for Apple MacBookPro (Intel Core Duo) on August 21, 2006.
Version August 8, 2006
The correction model adopted in CORRECT and XSCALE in the June 2006 release
turned out to be less robust than that of the older versions. For this
reason the old model was revived.
Version June 2006
-
The dynamic range of image pixel data that can be handled by XDS has
been increased to 20 bits (previously 18).
-
Faster execution of CORRECT and XSCALE, resulting from a new central
data structure more suitable for parallel execution (Openmp).
-
The CORRECT step has been modified to accept the additional input
parameter NBATCH=
which controls the number of absorption correction factors.
Consequently, the action of the input parameter
DELPHI=
is now confined to the INTEGRATE step and no longer used by CORRECT.
-
Bug fix in the reading routine of images from the saturn92 and RAXIS
detector.
-
Removal of restrictions for the total number of input files or
reflections that can be processed by XSCALE.
Version November 2005
Bug correction with respect to the August 2005 version
(released after August 16, 2005):
-
Bug fix for the ADSC Q315 detector when the image header exceeds 512 bytes.
Version August 2005
Changes and bug corrections with respect to the May 2005 version
(released after June 30, 2005):
-
XDS now accepts images in the STOE format (Stoe & Cie GmbH, Darmstadt,
Germany). To correct the images for spatial distortions a new parameter
was introduced,
STOE_CALIBRATION_PARAMETERS=.
The routine for reading images in the STOE format as implemented in
XDS is incomplete because pixel values above 65535 are always treated as
overflows.
-
The INTEGRATE and CORRECT steps of XDS as well as XSCALE now provide
Schwarzenbach and Flack's
psi-angle for each reflection which completely specifies diffraction
geometry with respect to the unit cell axes.
-
Correlation factors between observed and expected reflection profiles
reported near the end of INTEGRATE.LP have been incorrect and came out
too low (bug reported by Fred Vellieux, CNRS, Grenoble). The bug has no
consequences on the final data set.
-
The polarization correction factor was incorrectly calculated in the
INTEGRATE step. The effect on the final data set is likely to be
marginal in most situations. In case of doubt the INTEGRATE and CORRECT
steps should be repeated with the new version of XDS.
Version May 2005
Changes with respect to the previous version:
-
The DEFPIX step has been modified to accept the input parameter
EXCLUDE_RESOLUTION_RANGE=
that was used previously only by the CORRECT step. The new
feature allows to exclude ice-rings from the trusted region of
the detector surface prior to the integration process.
-
The INTEGRATE step has been substantially revised. Compared with the
previous versions it requires only a moderate virtual address space
even for very large data sets.
-
The COLSPOT and INTEGRATE steps of XDS have been modified to make
efficient use of Unix/Linux-clusters to reduce the wall-clock time
needed for data processing. It is no longer required that the
processors at each cluster node share the same address space. In
case they do, XDS can exploit additional data parallelism at a more
fine-grained level. The user can set (in XDS.INP) the number of nodes
in the cluster by the new input parameter
MAXIMUM_NUMBER_OF_JOBS=
-
Obsolete input parameters (causing xds to stop with an error message):
RMAX=
PROFILE_RANGE=
© 2005-2014, MPI for Medical Research, Heidelberg
Imprint.
Wolfgang.Kabsch@mpimf-heidelberg.mpg.de
page last updated: March 7, 2014