CBFlib );PILATUS pixel detector format
R-AXIS4 and SATURN92 CCD-detector format;
NOIR-1 detector format;
CCD-detector (1024 X 1024) at Brandeis & Brookhaven;
All input parameters needed for data processing are collected in the file named XDS.INP which must reside in the current directory where XDS will be invoked. File templates (examples) for XDS.INP are available for the detectors supported by XDS. Their use is strongly encouraged as they reduce input errors and simplify program usage. Many of the parameters are assigned default values that work fine in most cases and rarely need to be changed. Thus, running XDS amounts to just editing a few parameter values in the selected input file template (for example XDS-ADSC.INP if data images were recorded by the ADSC detector) and renaming the edited file into XDS.INP.
This chapter explains the meaning of all parameters used by the XDS
program. The parameters may be given in arbitrary order. Each parameter
name consists of a string of characters without intervening blanks or
exclamation marks and includes an equal sign as its last character. The
value must follow the parameter name on the same line. The parameter
names cannot be abbreviated; they are case sensitive, too. Characters
in a line to the right of an exclamation mark are comment.
The value of JOB= can be ALL (default) or any combination of the keywords described below. Each keyword names a subroutine to be executed.
Example: JOB=IDXREF DEFPIX XPLAN INTEGRATE CORRECT
XDS will execute the specified subroutines only and will skip the
previous steps XYCORR, INIT, COLSPOT. This saves time in cases XDS has
failed in a previous run in the IDXREF step because of a misindexing
problem and you like to try indexing alternatives.
This parameter specifies the maximum number of approximately equal portions of the data set that are each processed as an independent job by the computer system - thereby using available hardware to reduce the wall-clock time for execution of the COLSPOT and INTEGRATE steps of XDS. Up to 99 jobs are allowed. A value of one will be used if the parameter SECONDS= is greater than zero, meaning that data processing overlaps with data collection.
Each (COLSPOT or INTEGRATE) job runs on one (not necessarily the same) node in a networked (NFS) environment where each node may consist of several processors sharing identical address space under control of OpenMP. The jobs are independent processes that do not communicate at all. Moreover, all nodes of the cluster are controlled by a Unix/Linux operating system and use compatible conventions for binary files and number representations. In addition, the processors of each node can be used for parallel execution of all compute-intense steps of XDS (INIT,COLSPOT,IDXREF,INTEGRATE,CORRECT,XSCALE); this is controlled by the parameter MAXIMUM_NUMBER_OF_PROCESSORS=.
Example: MAXIMUM_NUMBER_OF_JOBS= 4
The set of collected data images is divided into approximately 4
equal portions that are each processed as an independent job by the
computer cluster during the COLSPOT and INTEGRATE steps. Given
sufficient hardware, these data processing steps will finish
almost 4 times earlier compared with the processing as one single job.
Parameter is used by COLSPOT, INTEGRATE.
This parameter defines the maximum number of cpus that can be employed by the parallel version of XDS (xds_par, xscale_par) for data processing by a single node of the computer cluster. The parallel version uses OpenMP for execution by a team of up to 99 threads and relies on a shared memory multiprocessor platform. Together with the parameter MAXIMUM_NUMBER_OF_JOBS= up to 99*99 cpus can be used. It is recommended to use defaults for these two parameters (see Example 1) as xds_par determines their optimal values from the given data set and the computer system. The parameter is ignored by the single processor version of XDS.
Example 1
!MAXIMUM_NUMBER_OF_PROCESSORS=99
!MAXIMUM_NUMBER_OF_JOBS=99
CLUSTER_NODES=bragg01 bragg02 bragg03 bragg04
!SECONDS= 0
!JOB=ALL
Default values are used for the parameters that are commented out.
In case of using the parallel version of XDS (xds_par)
the program first enquires the number of processors of the computer that can
be employed by OpenMP and assigns an approximately equal amount of the
necessary computations to each single cpu of each of the 4 nodes of the
cluster. At the end of each program step
the results obtained from each single process are combined.
NOTE, that XDS assumes that data collection is finished before
processing begins
so that all images are available (SECONDS=0 by default).
Example 2
MAXIMUM_NUMBER_OF_PROCESSORS= 4
MAXIMUM_NUMBER_OF_JOBS=16
SECONDS= 0
JOB=ALL
In the COLSPOT and INTEGRATE steps the set of data images is subdivided
into 16 approximately equal portions and each portion is processed by a
team of 4 cpus. In the INIT, IDXREF and CORRECT step, 4 cpus will be used.
Parameter is used by INIT, COLSPOT, IDXREF, INTEGRATE, CORRECT.
This parameter specifies the names of the nodes of the computer cluster you would like to run XDS. These nodes name a subset of the remote hosts in the NFS networked environment of your computer cluster where each host may comprise a shared memory multiprocessor system. In case of less than two specified nodes XDS will run on the peer node. At most 99 nodes may be specified using a total of at most 2048 characters.
The cluster nodes should use a network file system with common mountpoints, and allow command execution by ssh without asking for a password (see Installation on a computer cluster in downloading). The automatic distribution of the computations assumes cluster nodes of similar performance and identical number of cores.
Example: CLUSTER_NODES=bragg01 bragg02 bragg03 bragg04
XDS will automatically distribute processing of your data set among the
4 specified nodes in an optimal way. Other nodes of the cluster - if
they exist - are not used by XDS (as a courtesy to other users of
the cluster).
Parameter is used by COLSPOT, INTEGRATE.
Maximum number of seconds for XDS to wait until data image must appear (default is 0). If a positive parameter value is specified, XDS will enforce MAXIMUM_NUMBER_OF_JOBS=1, replacing any user input for this values.
Example: SECONDS=60
This allows you to start data processing by XDS while data collection
is still going on, but XDS cannot make use of all of the computing power
of the cluster.
Parameter is used by XYCORR, INIT, COLSPOT, INTEGRATE.
Defines size of RAM memory for storing a given number of data images in a cache to reduce disk transfers.
If this parameter is omitted a default value for the cache size is calculated that is just big enough to accomodate the images in a batch during the INTEGRATE step of XDS. To prevent excessive requests for cache memory, in particular when processing extremely fine-sliced data images, the cache size is limited in the XDS code to a total of 2^31-1 image pixels. If this limit is exceeded, only fewer images could be stored in the cache and a warning message is issued. For reasons of speed in processing the data set, the user could then stop this job and restart XDS after either
Example 1: NUMBER_OF_IMAGES_IN_CACHE=0
This turns off caching of data images completely.
Example 2: NUMBER_OF_IMAGES_IN_CACHE=500
The cache size is dimensioned to accomodate 500 images.
If the total number of images in the data set does not exceed this
number each image will be read only once during the complete processing.
On the other hand, for extremely fine-sliced rotation images
OSCILLATION_RANGE=0.01 °,
the size of the cache is just big enough to buffer the images in a
single batch covering a total rotation range of
DELPHI=5.0 °.
Parameter is used by INIT, COLSPOT, INTEGRATE.
Test flag for additional diagnostics and control images.
Parameter is used by XYCORR, INIT, COLSPOT, INTEGRATE.
Specifies the detector used for data collection. The parameter is used in the XYCORR step to select the method for computing spatial corrections appropriate for the detector. The parameter value can be:
Example: DETECTOR=CCDCHESS
If the MAR CCD or the CCD detector at CHESS was used for data
collection.
Parameter is used by XYCORR, INTEGRATE
Number of "fast" and "slow" pixels , respectively, in a data image. The "fast" direction runs along X and the "slow" direction along Y. A pixel at IX, IY in an image is found at address IADR= IX + NX*(IY-1). Consult Table of supported detectors for selection of the correct parameter values.
Parameters are used by XYCORR, INIT, COLSPOT, IDXREF
Size of "fast" and "slow" pixels (mm) along X and Y, respectively. The "fast" direction runs along X and the "slow" direction along Y. A pixel at IX,IY in an image is found at address IADR= IX + NX*(IY-1). Consult Table of supported detectors for selection of the correct parameter values.
Parameters are used by XYCORR, IDXREF
The contents of a detector pixel is an integer value proportional to the number of X-ray quanta reaching the pixel. The maximum value of this proportional range is specified by the mandatory input parameter OVERLOAD=. If a pixel contents exceeds this maximum value the pixel is overloaded; a reflection is overloaded if it includes one or more overloaded pixels. In the "INTEGRATE" step overloaded reflections are excluded from the determination of reference profiles. Otherwise they are treated like all other reflections and saved on the output file INTEGRATE.HKL. In the "CORRECT" step of XDS overloaded reflections are excluded from the final output because their integrated intensities are incorrect. However, the user always has the possibility to repeat the "CORRECT" step with a different value for OVERLOAD=. There is no default value. For selection of an appropriate parameter value for your detector consult Table of supported detectors.
Example: OVERLOAD=110000
If you had your data processed with a higher parameter value and are
afraid that some overloaded reflections are contaminating your final
data set, you could rerun just the CORRECT step (by specifying
JOB=CORRECT) with a smaller value for OVERLOAD=.
Parameter is used by INTEGRATE, CORRECT
Smaller pixel values in a data image are considered as invalid (not scanned). The default value is dependent on the detector used, which is 0 in most cases. NOTE, that a negative value is invalid.
Parameter is used by INIT, COLSPOT, INTEGRATE
Fraction of intensity loss per mm due to absorption in silicon. The absorption of x-rays depends on the wavelength; XDS will provide the appropriate value for silicon unless specified by the user. This parameter applies to the PILATUS or EIGER pixel detector which uses a silicon sensor for conversion of x-rays. Unlike CCD- and other detectors these pixel detectors use a finite silicon thickness (SENSOR_THICKNESS=0.32 mm) which makes it necessary to correct the reflection intensities for variations in the detection probability of the scattered x-rays. These variations result from different path length in the silicon sensor due to the oblique incidence of the diffracted beam.
Example: !SILICON=3.9
XDS will compute the correct value for the specified x-ray wavelength
since no positive value was given by the user. This is the recommended
procedure. Uncommenting this parameter (by removal of the exclamation mark)
would enforce XDS to use the value 3.9.
Parameter is used by XYCORR, CORRECT
Thickness (mm) of the detector's sensor used for conversion of x-rays. Unlike CCD-detectors which have typically a negligable value of about 0.01 mm, these pixel detectors use a finite silicon thickness of 0.32 mm. In the CORRECT step of XDS this parameter is used in conjunction with SILICON= to correct reflection intensities for variations resulting from different path length in the silicon sensor due to the oblique incidence of the diffracted beam. The default value of the parameter is 0.0 which should be used for all other detectors except for the PILATUS or EIGER pixel detectors.
Example: !SENSOR_THICKNESS=0.32
XDS will use the default value of 0.0 since this parameter was not
specified. This is recommended for all but the PILATUS pixel detector.
Uncommenting this parameter (by removal of the exclamation mark)
would enforce XDS to use the value 0.32 which is correct for the
PILATUS.
Parameter is used by XYCORR, CORRECT
Radial and tangential offset correction for spiral read-out scanners like MAR or MAC. At present XDS cannot determine these values and only computes a look-up table of spatial corrections from the given values (coming from somewhere else). Usually, both values are zero.
Parameters are used by XYCORR
This parameter is optional and has a meaning only for the STOE imaging plate spiral read-out detector (Stoe & Cie GmbH, Darmstadt, Germany). If specified, the parameter consists of 8 numbers, separated by at least one blank, from which the spatial correction tables X-CORRECTIONS.cbf and Y-CORRECTIONS.cbf are calculated in the XYCORR-step of XDS. The numbers must be given in the order as they appear in the crystal file produced by the manufacturer's software: DEL_R DEL_H DEL_X DEL_Y DEL_D EPS_X EPS_Y EPS_Z.
Example: STOE_CALIBRATION_PARAMETERS=-0.031 0.149 0.056 -0.278 -0.120 0.046 -0.375 0.491
The first 5 values are off-sets specified in mm while the last 3 values
refer to misalignment angles of the imaging plate given in °.
Parameter is used by XYCORR
File name and format of brass-plate image used in step XYCORR to calculate the spatial correction tables X-CORRECTIONS.cbf and Y-CORRECTIONS.cbf. This is mandatory for the SIEMENS detector. For the SIEMENS detector a brass grid plate is mounted on the detector face and the detector is moved to exactly the distance used later for data collection. An iron x-ray source is placed exactly at the place later occupied by the crystal (the origin of the laboratory coordinate system) and the detector response is collected for about 60 min (depends on the source) and saved on a file whose name is the input value of BRASS_PLATE_IMAGE=. Note, that a misplaced x-ray source will result into wrong correction values computed by XYCORR which might prevent a proper indexing of the diffraction spots.
Example: BRASS_PLATE_IMAGE= ../images/brs13cm HARVARD
Parameter is used by XYCORR
Grid distance (mm) between brass-plate holes. If specified, the given value overrides the default settings for the SIEMENS detector. For other detectors no defaults are available. They usually do not require a brass-plate image correction and the parameter HOLE_DISTANCE= will be ignored.
Parameter is used by XYCORR
Number of calibration holes of the brass-plate. If specified, the given value overrides the default settings for the SIEMENS detector. MXHOLE must always be <=1369. For other detectors no defaults are available. They usually do not require a brass-plate image correction and MXHOLE= is omitted from XDS.INP.
Parameter is used by XYCORR
Minimum number of calibration spots from the brass-plate that must be observed on the calibration image. If specified, the given value overrides the default settings for the SIEMENS detector. MNHOLE should be slightly larger than half of the number of calibration holes of the brass-plate. For other detectors no defaults are available. They usually do not require a brass-plate image correction and MNHOLE= is omitted from XDS.INP.
Parameter is used by XYCORR
File name and format of two correction tables used to compensate
the misorientations of the modules with respect to the X- and Y-axes of the
PILATUS pixel detector. Although these are specific for each instrument of this
type, they are independent of the detector's position and orientation.
Moreover, the corrections need to be determined only once (by the manufacturer)
as the modules do not change their place within the assembled detector.
The geometrically corrected coordinates of a pixel at IX,IY are found by
adding the table_value(IX,IY)/100.0 for the X- and Y-tables, respectively.
If both parameters are absent from XDS.INP the geometrical corrections are
assumed negligible.
Example:
X-GEO_CORR= GD_6M_X06SA_SLS_27022007_X.pck CCP4
Y-GEO_CORR= GD_6M_X06SA_SLS_27022007_Y.pck CCP4
The two geometrical correction files are located in the current directory
and given in CCP4 format layout.
Parameter is used by XYCORR
File name, access, and format of a dark-current (non-Xray background) image. This image will be used by "INIT" to generate a look-up table of the non-xray background at each pixel position. The table is saved in file "BLANK.cbf". The parameter is optional. If a dark-current image is not available, the table "BLANK.cbf" is generated either from the value of the parameter OFFSET=. For the SIEMENS detector, which has no dark current, the parameters OFFSET=, and DARK_CURRENT_IMAGE= are ignored.
Example: DARK_CURRENT_IMAGE= ../brown17_dark/dark_rc3_001 ESRF DIRECT
Parameter is used by INIT
This parameter value specifies the dark-current (non-Xray background) contents in each data image pixel. The default value is 0. As the SIEMENS detector has no dark current, this parameter will be ignored. If a dark-current image (see DARK_CURRENT_IMAGE=) is not available, the table "BLANK.cbf" is generated by "INIT" from the value of the parameter OFFSET=.
Parameter is used by INIT
The gain parameter value g relates the contents of a detector pixel p to the
equivalent number of X-ray quanta c seen by the pixel; i.e.
p = g × c + o
where o is the dark current offset
(see OFFSET=). This optional parameter can be used to
specify a single fixed conversion factor for all detector pixels. This may be
useful for a 'true' counter detector (like PILATUS).
Usually the gain value is
allowed to vary for each pixel and for this reason XDS does not provide
a default value for GAIN=. Instead a look-up table GAIN.cbf is determined in the INIT
step that contains the ratio between variance and mean of the pixel contents
in the neighbourhood of each image pixel.
Example: GAIN=1.0
For a true counter detector (like PILATUS) one could define GAIN=1.0.
Parameter is used by INIT
Inner (RMIN) and outer (RMAX) relative radii limiting the trusted region on the detector. The relative radius of a pixel at IX, IY is defined as R = sqrt{((IX-NX/2)/(NX/2))^2 + ((IY-NY/2)/(NY/2))^2}. The pixel at IX, IY is within the trusted region if RMIN < R < RMAX. Default is RMIN=0 and RMAX=1.0. This parameter provides a simple way of defining the acceptable detector surface in the INIT step. During the IDXREF step of XDS this parameter is checked again and only those spots are accepted that fall within the trusted region. Thus, in case IDXREF failed because of too many alien spots near the center of the image, the user could exclude these spots by an appropriate increase of RMIN and repeating IDXREF.
Example: TRUSTED_REGION=0.0 1.35
This includes the corners of the rectangular detector for data
collection.
Parameter is used by INIT, IDXREF
This allows you to remove a rectangle from the trusted detector plane.
The rectangle is specified by 4 numbers, namely the coordinates X1,X2
defining the X-interval and the coordinates Y1,Y2 defining the Y-interval
(pixel). A pixel at IX,IY will be classified as 'untrusted' if
X1 < IX < X2 and Y1 < IY < Y2. An arbitrary number (default 0)
of these parameters may be specified.
This parameter provides a simple way of defining the acceptable detector
surface by exclusion of bad rectangles which could have been caused by
malfunctioning hardware.
A single untrusted pixel at IX,IY can be excluded with
UNTRUSTED_RECTANGLE= IX-1 IX+1 IY-1 IY+1.
The pixel coordinates of the points defining the bad rectangle can be
found by looking with the XDS-Viewer program at the background
BKGINIT.cbf obtained from a preliminary run of INIT or from
BKGPIX.cbf generated by the DEFPIX step of XDS. Repeat DEFPIX if
necessary to exclude this bad region from subsequent integration.
Example: UNTRUSTED_RECTANGLE=570 1469 1920 2048
The rectangle with a "fast" (X-) pixel coordinate between 570 1469 and
a "slow" (Y-) coordinate between 1920 and 2048 is to be excluded
from data processing.
Parameter is used by INIT, DEFPIX
The 4 numbers X1,X2, Y1,Y2 of this parameter specify a rectangle of
detector pixels (X1,X2 define the X-interval and Y1,Y2 define the
Y-interval). Pixels covered by the largest ellipse that fits into
this rectangle are considered as 'untrusted'. An arbitrary number
(default 0) of these parameters may be specified.
This parameter provides a simple way of excluding pixel regions
shaded by the beam stop. The X- and Y-intervals can be found easily
by looking with the XDS-Viewer program at the background BKGINIT.cbf
obtained from a preliminary run of the INIT step of XDS. To exclude
this bad region rerun INIT (or DEFPIX) with the appropriate parameter
values.
Example: UNTRUSTED_ELLIPSE=570 1469 1920 2048
The largest ellipse that fits into the rectangle with a "fast" (X-)
coordinate between 570 1469 and a "slow" (Y-) coordinate between
1920 and 2048 will be excluded from data processing.
Parameter is used by INIT, DEFPIX
This parameter defines a convex quadrilateral by 4 corners
where each corner is specified by its X,Y pixel coordinates. Thus
8 numbers must be provided, separated by at least one blank character.
An interior point of the quadrilateral will always be seen on the same
side (either left or right) by a person walking along the lines
connecting the 4 corners in succession and coming back to the starting
point. Pixels that are interior points of the quadrilateral are
considered as 'untrusted'. An arbitrary number (default 0) of these
parameters may be specified.
This parameter provides a simple way of excluding shaded pixel regions
that cannot be enclosed by border lines parallel to the detector's
X and Y directions. The X,Y pixel coordinates of the 4 corners an be
found easily by looking with the XDS-Viewer program at the background
BKGINIT.cbf obtained from a preliminary run of the INIT step of XDS.
To exclude this bad region rerun INIT (or DEFPIX) with the appropriate
parameter values.
Example:
UNTRUSTED_QUADRILATERAL=565 1574 159 1552 1508 1533 566 1536
Pixels in the interior of the quadrilateral will be excluded from data
processing.
Parameter is used by INIT, DEFPIX
This parameter consists of a pair of numbers that are used by DEFPIX for defining untrusted detector pixels, which may result from shading parts of the detector. For recognizing these shaded regions, DEFPIX generates the control image ABS.cbf from the initial background table BKGINIT.cbf (obtained from the INIT step). The control image contains values around 10000 for unshaded pixels and lower values for shaded pixels. The default is VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000.
Values outside the specified range are treated as unreliable. Unreliable pixels are marked by -3 in the final background table BKGPIX.cbf and removed from the trusted detector region. The table BKGPIX.cbf should always be inspected with the XDS-Viewer program to see whether the excluded detector region makes sense. If you observe that some shaded regions are still included in BKGPIX.cbf, you may repeat the program step by specifying JOB= DEFPIX with a more appropriate value range, for example VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 7000 30000. However, if the value range has been chosen too tight, this may exclude also "good" regions from the detector and you have to repeat the procedure again.
Parameter is used by DEFPIX
An accepted reflection h, k, l must have a resolution
d(h,k,l)=λ/{2sinθ} within the specified Å range. Detector
pixels outside the specified resolution range are classified as
untrusted in the DEFPIX step and will not be used in the INTEGRATE and
CORRECT steps of XDS. Untrusted detector pixels are marked by -3 in the
table BKGPIX.cbf. To verify that the chosen resolution range is
appropriate you should always visually check BKGPIX.cbf with the XDS-Viewer
program.
The parameter is also used during the IDXREF step for limiting spots
used for lattice recognition and parameter refinements.
The parameter is also used by the CORRECT step of XDS. This may be useful if you want to exclude high resolution reflections beyond the diffraction limit of your crystal from the final output file XDS_ASCII.HKL. In this case you chose the appropriate resolution range and just repeat the CORRECT step of XDS (JOB=CORRECT).
Example: INCLUDE_RESOLUTION_RANGE= 20.0 0.0
This is the default range. The low resolution limit is 20.0 Å,
while the high resolution limit of 0.0 Å means that all recorded
reflections will be accepted.
Parameter is used by IDXREF, DEFPIX, CORRECT
Resolution range (Å) for excluding reflections. This feature
allows to remove ice-rings from the trusted region of the detector
(DEFPIX step) or from the final data set (CORRECT step). Unfortunately,
also good reflections in the specified resolution ranges are lost.
From 0, which is the default, up to an arbitray number of such ranges
may be specified. The parameter is also used by IDXREF for excluding
spots from lattice recognition and refinements.
Reflections of hexagonal ice are at 3.897, 3.669, 3.441, 2.671, 2.249 Å
(Thomas Schneider and Elspeth Garman, J.Appl.Cryst. 30, 211-237, 1997)
Example:
EXCLUDE_RESOLUTION_RANGE= 3.93 3.87 ! ice-ring at 3.897 Å
EXCLUDE_RESOLUTION_RANGE= 3.70 3.64 ! ice-ring at 3.669 Å
EXCLUDE_RESOLUTION_RANGE= 3.47 3.41 ! ice-ring at 3.441 Å
EXCLUDE_RESOLUTION_RANGE= 2.70 2.64 ! ice-ring at 2.671 Å
EXCLUDE_RESOLUTION_RANGE= 2.28 2.22 ! ice-ring at 2.249 Å
All reflections with a resolution within any of the specified five
ice-rings are excluded in the IDXREF DEFPIX and CORRECT steps.
Parameter is used by IDXREF, DEFPIX, CORRECT
A reciprocal lattice point crosses the Ewald sphere by the shortest route if the crystal rotates about a (virtual) axis perpendicular to both the diffracted and incident beam wave vectors. Thus, rotation around a fixed axis as enforced by the rotation method leads to an increase of the path length through the Ewald sphere by a factor 1/ZETA. ZETA is the cosine of the angle between virtual and actual rotation axes and is closely related to the reciprocal Lorentz factor. For reflections near the 'blind region' close to the actual rotation axis, ZETA will become very small. This leads to excessively large and thereby inaccurate correction factors for the integrated intensity of such a reflection. The user can exclude these reflections by selecting a suitable lower bound for ZETA; the default is MINIMUM_ZETA=0.05 allowing reflections very close to the spindle axis.
Example:
MINIMUM_ZETA= 0.15
Compared to the default value this choice will lead to a less complete
data set by omitting more unreliable reflections close to the 'blind region'.
Parameter is used by XPLAN, INTEGRATE, CORRECT
File name template and format (optional) of the data images.
The file name contains several consecutive question marks (see examples). For accessing a specific data image, XDS will substitute the appropriate image number for the question marks in the file name template. To save space it is allowed to compress the images by using the UNIX compress, gzip, or bzip2 routines. On data processing XDS will automatically recognize and expand the compressed images files. The file name extensions (.Z, .z, .gz, bz2) due to the compression routines should not be included in the file name template.
The name template may be followed by a keyword specifying the format of the data image files. For most of the detectors presently used the image format is recognized automatically by XDS and a format keyword, like MAR or GENERIC in the examples below, is not needed. However, if the format is explicitly named, XDS will attempt to read the image in the specified way. The format keyword applies to all data images with the given file name template. The format KEYWORD can be:
CBFlib );
Example 1:
NAME_TEMPLATE_OF_DATA_FRAMES= ../data_images_??????.h5 GENERIC
DATA_RANGE=1 1234
LIB=name_of_external_library
This is the generic method used for accessing images. It relies on
an external library LIB. The library in this example is provided by
the manufacturer of the EIGER detector (DECTRIS AG, Basel).
Data of the first and last image of the data range are specified by
../data_images_000001.h5 and ../data_images_001234.h5 where the six
question marks are replaced by the image number (with leading zeros).
The specified image data are retrieved by the external library
routine. The format specifier GENERIC may be omitted. Details of the
method used by the library routine are irrelevant to XDS.
In the case of the EIGER detector, the external software
constructs the name of a master file, ../data_images_master.h5,
from the given name template by replacing the 6 question marks by the
string master. This file contains a list of file
names, each denoting a block of data from 100 detector images.
Example 2:
NAME_TEMPLATE_OF_DATA_FRAMES= ../mckhg_???.image MAR
This is the usual method of specifying images for processing images by XDS. The optional format keyword MAR refers to images from an old MAR spiral read-out scanner. The reading routine required is automatically recognized from the data image and included in the XDS software. The keyword MAR could have been omitted.
Parameter is used by INIT, COLSPOT, IDXREF, INTEGRATE
This optional parameter specifies the name of an external, dynamically
linked library routine for reading images. It uses the
generic_data_plugin module provided at
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/LIB
http://cims.nyu.edu/~donev/Fortran/DLL/DLL.Forum.txt.
The possibility to link a dynamic library renders XDS more independent
of the technical details of future detector image formats.
Parameter is used by INIT, COLSPOT and INTEGRATE.
Numbers of first and last data image that are to be excluded from processing. An arbitrary number of such parameters can be specified in XDS.INP. This offers a simple way to specify corrupted images stored in a container format (like EIGER images).
Example: EXCLUDE_DATA_RANGE= 7 9 EXCLUDE_DATA_RANGE=99 99
The data images 7,8,9 and 99 will not be processed by XDS.
Parameter is used by INIT, COLSPOT, INTEGRATE, CORRECT
Numbers of first and last data image collected (must be >0).
Example: DATA_RANGE= 2 456
The data images 2, 3, ..., 456 will be processed by XDS. For accessing
the images the question marks in the generic file name template are
substituted by the image numbers in succession.
Parameter is used by COLSPOT, INTEGRATE, CORRECT
Numbers of first and last data image for determining the initial background. If this parameter is omitted, XDS will use images covering a total rotation range of 5° starting with the first data image collected.
Example: BACKGROUND_RANGE= 2 6
The initial background table BKGINIT.cbf will be determined from the
data images 2, 3, ..., 6.
Parameter is used by INIT
The background region of the detector surface consists of one or more islands surrounded by 'untrusted' pixels. The parameter sets a lower limit on the size of each island considered to be useful for data processing. This limit is specified as a fraction of the size of the largest background region.
Example: MINIMUM_FRACTION_OF_BACKGROUND_REGION=0.01
This is the default and rarely needs to be changed. Background islands
covering less than 1% of pixels compared to the largest island are
treated as unreliable and excluded from data processing.
Parameter is used by INIT
Numbers of the first and last data image used for locating strong spots in the COLPROF step. An arbitrary number of such ranges may be specified. Spots located in the specified images are saved in file SPOT.XDS. The default value of the parameter is: if SECONDS=>0 then SPOT_RANGE=BACKGROUND_RANGE else SPOT_RANGE=DATA_RANGE
The SPOT_RANGE= parameters are used also in the IDXREF step for selecting a subset of spots from file SPOT.XDS for indexing. In case the IDXREF step, based on all of the spots in file SPOT.XDS, was not successful, this step could easily be repeated with spots from the first few images, for example, after appropriate change of the SPOT_RANGE= parameters without the need to run COLSPOT again.
Example:
SPOT_RANGE= 1 10
SPOT_RANGE= 21 32
SPOT_RANGE= 45 60
SPOT_RANGE= 70 70
Images 1 to 10, 21 to 32, 45 to 60, and image 70 will be searched for
strong spots during the COLSPOT step. If the crystal has not slipped during
data collection it is advisable to use images from all parts of the data set.
The diffraction parameters determined by the subsequent IDXREF step are then
more reliable if based on spots distributed over a large total rotation
range. If the IDXREF step failed, the user could specify SPOT_RANGE= 21 70
and rerun IDXREF thereby omitting spots from the first 10 data images where
the crystal may have slipped.
Parameter is used by COLSPOT, IDXREF
These parameters are used to specify the alignment setting of the detector
with respect to the laboratory coordinate system.
Orientation of the detector is defined by the first two parameters: two
orthogonal vectors that - together with their cross product - define a
rotation matrix ED.
DIRECTION_OF_DETECTOR_X-AXIS=ED(1,1) ED(2,1) ED(3,1)
DIRECTION_OF_DETECTOR_Y-AXIS=ED(1,2) ED(2,2) ED(3,2)
ED(:,3)=ED(:,1) X ED(:,2)
These 3 vectors, {ED(:,1), ED(:,2), ED(:,3)}, form the right-handed
orthonormal detector system. It serves as a reference frame for
the specification of the arrangement of the detector components (segments)
which makes the description invariant to movements of the instrument.
The position of the detector, defined as origin vector to the point
0 0 0 of the detector system that is fixed in the
instrument, is specified (mm) in the laboratory coordinate system
by the vector
-ORGX*QX*ED(:,1)-ORGY*QY*ED(:,2)+F*ED(:,3)
using conversion factors
QX
QY.
This parametrization is used for reasons of compatibility with older
versions of XDS (before March 30, 2013).
NOTE, that the parameter value DETECTOR_DISTANCE=F
will be negative if ED(:,3) points towards the crystal.
The origin vector is a refinable parameter if requested by the keyword POSITION in the parameters REFINE(IDXREF)=, REFINE(INTEGRATE)=, or REFINE(CORRECT)=. This type of refinement treats the detector as a rigid body.
Default values for the above parameters are provided by the XDS.INP templates for most of the detectors. For the SIEMENS detector, or other detectors that can be rotated out, the situation requires a more detailed discussion (see COORDINATE SYSTEMS).
Example:
NX=1200 NY=1200 QX=0.15 QY=0.15
DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
ORGX= 605.0 ORGY= 592.0 DETECTOR_DISTANCE= 330.1
This is a typical description for an old MAR-scanner consisting
of a single segment of NX=1200 "fast" and NY=1200
"slow" pixels with a pixel size of
QX=
QY=0.15 mm.
By default, the single segment coincides with the detector plane
at the same origin with the "fast" pixel direction along
the detector x-axis.
The scanner is aligned with the detector coordinate system coinciding
with the laboratory system. The incident beam runs approximately
along the laboratory z-axis intersecting the detector plane at its
center at a distance of F=+330.1 mm. Note the positive sign because
the detector normal points away from the crystal.
A pixel at IX,IY on the detector (found at address IX+NX*(IY-1) in
the data image file) has the laboratory coordinates
x=QX*(IX-ORGX)*ED(1,1)+QY*(IY-ORGY)*ED(1,2)+F*ED(1,3)
y=QX*(IX-ORGX)*ED(2,1)+QY*(IY-ORGY)*ED(2,2)+F*ED(2,3)
z=QX*(IX-ORGX)*ED(3,1)+QY*(IY-ORGY)*ED(3,2)+F*ED(3,3)
Parameters are used by XYCORR, IDXREF
A detector is considered to consist of one or several rectangular segments at some arbitrary but fixed arrangement with respect to the detector system. Each segment is specified by the above set of seven mandatory parameters.
Each segment of the detector is specified by its own set of 7 parameters.
This way quite sophisticated instruments, like the cylindrical detector at the
long-wavelength beam line at DIAMOND, can be handled by XDS.
For single-segment detectors, all of the above 7 segment parameters can
be omitted from XDS.INP because the segment coordinate
system is identical with the detector system by default.
Example:
NX=1200 NY=1200 QX=0.15 QY=0.15
DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
ORGX= 605.0 ORGY= 592.0 DETECTOR_DISTANCE= 330.1
SEGMENT=1 1200 1 1200
REFINE_SEGMENT=
DIRECTION_OF_SEGMENT_X-AXIS= 1.0 0.0 0.0
DIRECTION_OF_SEGMENT_Y-AXIS= 0.0 1.0 0.0
SEGMENT_ORGX=0.0
SEGMENT_ORGY=0.0
SEGMENT_DISTANCE=0.0
This is a typical description for an old MAR-scanner consisting
of a single segment of NX=1200 "fast" and NY=1200
"slow" pixels with a pixel size of
QX=
QY=0.15 mm.
Note that the segment coordinate
system is identical with the detector system so that
the "fast" pixels run along the detector x-axis and the
"slow" pixels along the detector y-axis.
The parameters specifying segment values are default and could have
been omitted from XDS.INP.
Parameters are used by XYCORR, INIT, COLSPOT, IDXREF
Direction cosines of the rotation axis with respect to the laboratory system. The length of this vector will be normalized by XDS. The direction of the axis is chosen to describe a right-handed rotation. A default parameter value is provided by the XDS.INP templates.
Example:ROTATION_AXIS= 0.0 1.0 0.0
The rotation axis points along the laboratory y-axis. When looking
along the axis, the crystal would rotate clockwise when proceeding to
the next data image.
Parameter is used by IDXREF
Oscillation range of each data image in °. It must be a positive multiple of 0.0001. Thus, a value like 0.000125 would be incorrect! XDS assumes a right handed rotation of the crystal about the rotation axis when proceeding to the next data image. No sensible default value can be provided and the user must insert the correct value. For detectors with no read-out noise like the PILATUS an optimal choice for the oscillation range would match half of the crystal's mosaicity (defined as the standard deviation of the reflecting range). A further reduction of the oscillation range could lead to problems in the accurate determination of extremely low background and unreliably processed data.
Example: OSCILLATION_RANGE=0.1
This describes a "fine-sliced" data set with each image
covering an oscillation range of 0.1 °.
Parameter is used by IDXREF
These two parameters (together with the parameter OSCILLATION_RANGE=)
define the "phi"-angle the crystal has been rotated
about the spindle axis prior to recording data on image number i by
phi(i) = STARTING_ANGLE + OSCILLATION_RANGE * (i -
STARTING_FRAME)
The components of the unit cell vectors of the crystal with respect to
the laboratory coordinate system as reported by IDXREF, XPLAN,
INTEGRATE, and CORRECT refer to phi=0.0, that is to the
unrotated crystal. Obviously, the optimal data collection strategies
proposed by XPLAN depend on the two parameter values STARTING_ANGLE=
and STARTING_FRAME= as well.
In principle, knowledge of the "true" spindle dial setting is
not necessary and any fantasy value would work equally well. However,
it is better to specify the correct spindle angle as this allows you to
use absolute phi-angles when moving the crystal to the
starting position for optimal data collection predicted by XPLAN.
Example:
STARTING_ANGLE=0.0
STARTING_FRAME=first data image (as specified by DATA_RANGE=)
These are the defaults assumed by XDS when you omit the parameters from
XDS.INP. Thus the crystal orientation reported by IDXREF, XPLAN,
INTEGRATE, and CORRECT refers to the spindle position at the start of
the first data image and not to the true spindle dial setting.
This should be remembered when following the suggestions for optimal
data collection proposed by XPLAN.
Parameters are used by IDXREF
The parameter value consists of a number triple that specifies first, last and increment of the various starting spindle angles for the crystal rotation to be searched by XPLAN for pinpointing an optimal data collection strategy.
Example: STARTING_ANGLES_OF_SPINDLE_ROTATION=0.0 180.0 10.0
This is the default value assumed by the parameter. XPLAN estimates the
completeness of a data set of a fixed size of total rotation if data
collection began at phi=0, 10, 20, ..., 180 °. Note,
that the phi values may not refer to the true spindle dial
setting in case the defaults for the parameters STARTING_ANGLE= and
STARTING_FRAME= have been used.
Parameter is used by XPLAN
The parameter characterizes a grid of data sets of varying sizes for analysis by XPLAN. The grid is parameterized by a number triple that specifies minimum size, maximum size, and size increment (degrees of total rotation about the spindle axis). XPLAN determines the maximal completeness that could be obtained for a data set of a given size.
Example:
TOTAL_SPINDLE_ROTATION_RANGES=30.0 120.0 30.0
STARTING_ANGLES_OF_SPINDLE_ROTATION=0.0 180.0 10.0
These are the default values for the two parameters. XPLAN will
pinpoint an optimal starting angle selected from the grid phi=0,
10, 20, ..., 180 degrees if the data set covers 30 degrees of total
rotation, and repeats the analysis for data set sizes of 60, 90, and
120 degrees of total rotation.
Parameter is used by XPLAN
Resolution shell limits (Å). Only the high resolution limit of each shell is given. Up to 13 resolution shells will be accepted. The shell limits must be specified in decreasing order. The resolution shells are used by XPLAN to report the completeness of the various hypothetical data sets as a function of resolution. If the parameter is omitted (default) the high resolution limit that can be recorded by the detector is used.
Example:
RESOLUTION_SHELLS=20.0 10.0 6.0 3.0
Completeness will be reported for the resolution shells infinity-20.0,
20-10, 10-6, and 6-3 À.
Parameter is used by XPLAN
X-ray wavelength of the incident beam (Å). There is no default value and the user must insert the correct value.
Example: X-RAY_WAVELENGTH=0.92
A synchrotron data set collected at wavelength 0.92 Å.
Parameter is used by IDXREF
x, y, z components of the incident beam direction with respect to the laboratory coordinate system. The vector points from the source towards the crystal. The length of the vector is normalized by XDS. The parameter value will be refined in the course of data processing. Default starting values are provided by the XDS.INP templates.
Example: INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
The incident beam direction points along the laboratory z-axis.
Parameter is used by IDXREF
Fraction of polarization of direct beam in a plane specified by its normal. (0 < FRACTION_OF_POLARIZATION < 1). If omitted, the beam is assumed to be unpolarized, and a parameter value of 0.5 is used. For a negative value of FRACTION_OF_POLARIZATION or a value larger than 1 no polarization correction is carried out.
Example : FRACTION_OF_POLARIZATION=0.9
A typical parameter value for data collection at a synchrotron. In case
you want to try out different values, all you have to do is to repeat
the CORRECT step of XDS (JOB=CORRECT) with the chosen parameter values.
Parameter is used by CORRECT
x, y, z components of the polarization plane normal with respect to the laboratory coordinate system.
Example 1:
FRACTION_OF_POLARIZATION=0.5
POLARIZATION_PLANE_NORMAL= an arbitrary vector
For an unpolarized beam hitting the crystal there is no polarization plane.
Example 2:
FRACTION_OF_POLARIZATION=[cos(2*thetaM)]**2/[1+(cos(2*thetaM))**2]
POLARIZATION_PLANE_NORMAL= components of the monochromator diffraction
plane normal.
For a monochromator with incident unpolarized beam.
Example 3:
FRACTION_OF_POLARIZATION=0.0
POLARIZATION_PLANE_NORMAL= 0 0 0
This makes no polarization correction at all.
Example 4:
POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0
FRACTION_OF_POLARIZATION=0.95
The electrical field vector of the incident beam is found in the
x,z-plane of the laboratory coordinate system with a probability of 0.95.
Parameter is used by CORRECT
Fraction of intensity loss per mm due to air absorption. Each reflection intensity is multiplied by exp(|AIR*F*(1/cos(oblique angle)-1)|). The oblique angle is between the diffracted beam and the detector normal and assumes values 0...<90 °.
The absorption of x-rays by air depends on the wavelength; XDS will provide the appropriate value unless specified by the user. A negative value given by the user is ignored and the parameter is treated as unspecified.
Example: !AIR=0.001
XDS will compute the correct value for the specified x-ray wavelength
since no value was given by the user. This is the recommended procedure.
Uncommenting this parameter (by removal of the exclamation mark in this
example) would enforce XDS to use the value 0.001.
Parameter is used by CORRECT
Space-group number of the crystal. The numbers corresponding to each
possible space group are defined in the "INTERNATIONAL TABLES
I". All 230 space groups are implemented. From the space group
number and the unit cell parameters XDS provides a standard set of
symmetry operators; for space groups (like P2/c) with several cell
choices it may be necessary to make use of the reindexing facility of
XDS (parameter REIDX=) to select the cell choice appropriate to the
given symmetry operators.
In case a reindexing transformation is used in the CORRECT step,
the space group symmetry refers to the new cell.
A parameter value of zero indicates that space group and cell
parameters are unknown. XDS will try to find a reduced cell (step
"IDXREF") from the given spot list and continue in the
triclinic space group P1. Note, that in this case the results
reported in the XPLAN step are likely to be incorrect unless the
crystal is indeed triclinic!
Example: SPACE_GROUP_NUMBER=77
This specifies the tetragonal space group P42
Parameter is used by IDXREF, CORRECT
Unit cell parameters a, b, c (Å) and α, β, γ
(°). The cell constants must meet the requirements implicated by
the space group. First and second setting of monoclinic crystals must
be distinguishable by the cell constants. The cell parameters will be
ignored for an unknown space group.
In case a reindexing transformation is specified, the unit cell parameters
refer to the new cell.
Example:
UNIT_CELL_CONSTANTS=125.9 125.9 144.7 90.0 90 90
SPACE_GROUP_NUMBER=77
This specifies the cell constants of a tetragonal crystal obeying P42
space group symmetry. Note that the a and b axes must have identical
length and all angles must be exactly 90 ° as required by the
space group.
Parameter is used by IDXREF, CORRECT
Components of the unit cell basis vectors (Å) with respect to
the laboratory coordinate system for the unrotated crystal. If specified
XDS tries (in IDXREF and CORRECT) to find a unit cell basis close to the given
one that explains the observed diffraction spots. Purpose of this
feature is to maintain a consistent indexing scheme between several data
sets taken from the same crystal in the same orientation.
The unit cell basis vectors are accepted only if a space group is specified;
the cell constants are then derived from the basis vectors.
Example:
SPACE_GROUP_NUMBER=77
UNIT_CELL_A-AXIS= 3.554030 -92.080681 85.950844
UNIT_CELL_B-AXIS= 125.741653 7.675818 3.023864
UNIT_CELL_C-AXIS= -8.532763 98.197212 105.553246
This specifies the unit cell basis vectors of the unrotated crystal
by three numbers, namely the X-, Y-, Z-coordinates (Å) with respect to
the laboratory system. The cell constants are computed from the basis
vectors.
Parameters are used by IDXREF, CORRECT
The reindexing transformation consists of 12 integers that relate the
original indices H,K,L from file INTEGRATE.HKL to the indices H',K',L'
with respect to the new cell.
H'=(REIDX(1)*H+REIDX( 2)*K+REIDX( 3)*L)/IDXV+REIDX( 4)
K'=(REIDX(5)*H+REIDX( 6)*K+REIDX( 7)*L)/IDXV+REIDX( 8)
L'=(REIDX(9)*H+REIDX(10)*K+REIDX(11)*L)/IDXV+REIDX(12)
The value of the integer IDXV depends on the lattice type used for
specifying reflections on file INTEGRATE.HKL; IDXV is
1 for a primitive,
2 for a face or body centred,
3 for a rhombohedral,
4 for a lattice centred on all faces.
IDXV is set by XDS and cannot be input by the user.
The capability for reindexing reflections allows the user to process a data set even if space group and cell constants of the crystal are unknown. On completion of XDS, when integrated intensities are available, the user could then test plausible space groups by just repeating the CORRECT step (JOB=CORRECT) together with the corresponding reindexing transformation and conventional cell parameters listed in CORRECT.LP.
Example
REIDX= 0 -1 0 0 -1 0 0 0 0 0 -1 0
SPACE_GROUP_NUMBER=77
UNIT_CELL_CONSTANTS=125.9 125.9 144.7 90.0 90 90
JOB=CORRECT
This example illustrates the final step of processing data from a
crystal of initially unknown space group symmetry and cell constants.
First, a complete run of XDS was carried out with the crystal described
by a triclinic reduced cell which has been automatically determined in
the IDXREF step. In the CORRECT step space group P4 (#75) was automatically
determined together with strong indications for a twofold screw axis.
It was decided to repeat the CORRECT step now in space group
P42(#77) with cell constants and reindexing
transformation taken from the CORRECT.LP output.
The new reflection indices are related to
the old, triclinic H, K, L by the transformation H'=-K,
K'=-H, L'=-L. Note, that the cell constants have to be
"clean"; that means they have to satisfy the constraints of
the symmetry group.
Parameter is used by CORRECT
The parameter value can be either TRUE or FALSE indicating whether Friedel's law holds true or not. Clearly, the completeness of data as reported by XPLAN and CORRECT depends on whether reflections h, k, l and -h,-k,-l are considered to be equivalent or not. For anomalous data of low redundancy CORRECT could even fail to determine R-factors and reasonable values for the empirical error model.
Example: FRIEDEL'S_LAW=TRUE
This is the default value. Reflections h, k, l and -h,-k,-l are
considered to be equivalent.
Parameter is used by XPLAN, CORRECT
These two decision constants are used for detection of lattice symmetry. They set an upper limit on the deviations between the unconstraint unit cell parameters and their closest approximation satisfying a proposed lattice symmetry. If the deviations exceed one or both limits XDS assumes that the crystal does not possess the tested lattice symmetry. The angle error is specified in degrees.
Example: MAX_CELL_AXIS_ERROR=0.03 MAX_CELL_ANGLE_ERROR=2.0
These are the default values for the parameters. Thus, for an observed set
of cell parameters like a=65.3 b=66.0 c=180.4 α=90.1 β=89.5
γ=119.3,
we cannot reject the hypothesis that the lattice could be hexagonal because
max{|a-(a+b)/2|,|b-(a+b)/2}<0.03*(a+b)/2 and
max{|α-90|,|β-90|,|γ-120|}<2.
Parameters are used by IDXREF, CORRECT
Resolution range (Å) for including reflections in the calculation of Rmeas (Diederichs and Karplus, 1997) when analysing the intensity data for space group symmetry in the CORRECT step.
Example: TEST_RESOLUTION_RANGE= 10.0 5.0
This is the default value.
Strong data between 10 to 5 Å resolution are used for the tests in order
to obtain a strong contrast in the Rmeas values between
correct and incorrect choices for the space group.
Parameter is used by CORRECT
Defines a minimum number of reflections (from the TEST_RESOLUTION_RANGE=) needed to calculate a reliable estimate for Rmeas in the CORRECT step.
Example: MIN_RFL_Rmeas=50
This is the default value for the parameter.
Parameter is used by CORRECT
This parameter is used in the CORRECT step for identification of possible space groups. It controls the upper limit for acceptable Rmeas as a multiple of the lowest Rmeas found for all tested space groups. If Rmeas is larger than this upper limit, the corresponding space group symmetry is considered violated by the observed data. Among all tested space groups XDS will select that group that requires a minimum number of unique reflections to account for the observed intensities at an acceptable Rmeas.
Example: MAX_FAC_Rmeas=2.0
This is the default value for the parameter. If we assume that the lowest
Rmeas=5.8 was found when testing triclinic space group P1
the upper limit for acceptable Rmeas would be 2*5.8=11.6.
Parameter is used by CORRECT
The box of size (2*NBX+1)*(2*NBY+1) is centered in succession at each pixel of the images specified for background determination and the pixel variation within the box is determined. The results are used to estimate the expected variation in a data image in the absence of any spot and saved in the look-up table GAIN.cbf. The comparison between the observed and expected pixel variation serves to distinguish "strong" from background pixels.
Example: NBX=3 NBY=3
These are the default values for the parameters.
Parameters are used by INIT
An image pixel belongs to the background region if the variation in the pixel contents of neighbouring pixels (region defined by NBX= and NBY=) does not exceed the specified number of standard deviations. Background pixels are not included in the localization of strong spots by COLSPOT and are not used for calculating Bragg-peak centroids in the INTEGRATE step.
Example: BACKGROUND_PIXEL=6.0
This is the default value for the parameter. The pixel at IX, IY is in
the background region, if the variation in contents of pixels within
the region IX-NBX,IX+NBX; IY-NBY,IY+NBY does not exceed the expected
variation by more than a factor of 6.
Parameter is used by COLSPOT, INTEGRATE
A 'strong' pixel to be included in a spot must exceed the background by more than the given multiple of standard deviations.
Example: STRONG_PIXEL=3.0
This is the default value for the parameter.
Parameter is used by COLSPOT
This value is an approximate upper limit for the total number of 'strong' pixels in all of the images scanned by COLSPOT. If this number is exceeded, COLSPOT will automatically raise the threshold used for classifying a 'strong' pixel.
Example: MAXIMUM_NUMBER_OF_STRONG_PIXELS=1500000
This is the default value for the parameter which is usually sufficient
for COLSPOT to pick-up a large number of spots.
Parameter is used by COLSPOT
This allows to suppress spurious, isolated 'strong' pixels from entering the spot list generated by "COLSPOT".
Example: MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=6
This is the default value for the parameter.
Parameter is used by COLSPOT
This parameter serves to eliminate spots whose location of the maximum deviates by more than the specified parameter value from the centroid of the spot (pixel units).
Example: SPOT_MAXIMUM-CENTROID=3.0
This is the default value for the parameter.
Parameter is used by COLSPOT
The pixel contents must exceed the background by more than the specified value of standard deviations to be included in the calculation of the Bragg-peak centroid.
Example: SIGNAL_PIXEL=3.0
This is the default value for the parameter.
Parameter is used by INTEGRATE
This parameter controls the addition of partial intensity contributions
to the same reflection from adjacent image batches. The difference
between the image numbers (where each part of the reflection was recorded)
is weighted by the reciprocal Lorentz factor and compared with the
parameter value. If this weighted difference exceeds the parameter value
the reflections are not added. Instead, they are treated as separate
measurements with their missing parts being estimated by profile fitting.
This situation arises from processing the data set
in batches of images covering a small range of spindle rotation. The
crystallographic parameters are refined in each batch which could lead
to small deviations in the locations of the parts of a reflection
residing near a batch boundary. The weighting by the reciprocal Lorentz
factor allows a greater tolerance to reflections close to the spindle
axis.
Example: MAXIMUM_IMAGE_GAP_FOR_ADDING_PARTIALS=5.0
This is the default value for the parameter.
Contributions with identical h,k,l recorded less than 5.0/RLP images
apart are added. Typically, the reciprocal Lorentz factor ranges
0.05 ≤ RLP ≤0.5.
Parameter is used by INTEGRATE
Grid size (1/Å) of the histogram for finding difference vector clusters. If omitted a default grid size is estimated from the distribution of the diffracted beam wave vectors corresponding to the observed strong spots used for the IDXREF step.
Example: RGRID=0.0001
A grid size of 0.0001 (1/Å) is enforced instead of the
default.
Parameter is used by IDXREF
Minimum distance between diffraction spots required when depositing their vector difference in the histogram. This distance is specified in multiples of the length of one pixel. The reciprocal space equivalent of the length of a detector pixel is assumed as SQRT(QX*QY)/(F*λ). For a multi segment detector the largest distance F of any pixel from the crystal is taken.
Example: SEPMIN=7.0
This is the default value for the parameter.
Parameter is used by IDXREF
Maximum radius of a difference vector cluster (pixel units). A difference vector belongs to the cluster if its distance to the cluster centroid is less than CLUSTER_RADIUS=.
Example: CLUSTER_RADIUS=3.5
This is the default value for the parameter. The value is typically
chosen slightly smaller than 0.5 ×SEPMIN=
Parameter is used by IDXREF
Maximum allowed deviation from 'integerness' of computed indices of a reflection. This parameter corresponds to ε in Kabsch, 1993.
Example: INDEX_ERROR=0.05
This is the default value for the parameter. The default value works
fine and hardly needs to be changed.
Parameter is used by IDXREF
Maximum magnitude of index differences between reflections. This parameter corresponds to δ in reference Kabsch, 1993.
Example: INDEX_MAGNITUDE=8
This is the default value for the parameter. The default value works
fine and hardly needs to be changed.
Parameter is used by IDXREF
Minimum quality of indices required for a reflection to be included in the shortest tree.
The 3 parameters INDEX_ERROR=, INDEX_MAGNITUDE=, and INDEX_QUALITY= are used to control the local indexing of reflections by the shortest tree algorithm (Kabsch, 1993). Computed reflection indices deviating from integers by more than INDEX_ERROR= or indices of an absolute value larger than INDEX_MAGNITUDE= are given a penalty which lowers their index quality. Reflections are connected by a shortest tree. This tree is split into subtrees by removing unreliable connections with a value less than INDEX_QUALITY= (a number between 0 ... 1).
Example: INDEX_QUALITY=0.8
This is the default value for the parameter. The default value works
fine and hardly needs to be changed.
Parameter is used by IDXREF
The 3 values are added to the indices of the reflections in the "IDXREF" step. This allows to control critical indexing problems. Experience has shown that the detector origin (ORGX=, ORGY=) and the direction of the incident beam (INCIDENT_BEAM_DIRECTION=) are often specified with insufficient accuracy, which could easily lead to a misindexing of the reflections by a constant offset. For this reason, IDXREF considers alternative choices for the index origin and reports their likelihood for being correct (see file IDXREF.LP).
Example 1: INDEX_ORIGIN= 0 0 0
This is the default value for the parameter.
Example 2:
INDEX_ORIGIN=-1 0 0
JOB=IDXREF
Assume that the previous run (Example 1) using the default has stopped
in the IDXREF step with an error message. What could you do? Inspection
of the output from this step (IDXREF.LP) indicates that the h-indices
of all reflections could be off by 1. You could try to cure the problem
by just repeating the IDXREF step and adding -1 to the h-indices of the
reflections, which amounts to change in XDS.INP the two parameters by
the values given in Example 2.
Parameter is used by IDXREF
This parameter is used in the IDXREF step if the unit cell is unknown.
In this case an initial lattice basis is derived from clusters of
short difference vectors computed from the observed spots.
The difference vectors are considered as nodes of a mathematical
tree which are assigned to subtrees each with consistent indexing
with respect to the initial lattice basis.
It may happen that the roots of the subtrees differ by a constant
vector offset in reciprocal space.
These offsets as well as the initial basis can be accounted for by
construction of a new, augmented lattice basis.
The parameter MERGE_TREE= allows the user to control inclusion of the various subtrees into the augmented reciprocal lattice. The parameter defines a minimum required fraction of members in a subtree eligible for inclusion. Subtrees merged into a single lattice basis are marked by an asterisk * in IDXREF.LP. Note that inclusion of minor trees could lead to an augmented lattice basis that might even prevent recognition of the correct unit cell and crystal symmetry.
Example: MERGE_TREE= 0.2
This is the default value for the parameter. Compared with the main set,
subsets of clusters accounting for more than 20% of difference vectors
are merged into a new, common reciprocal basis.
Parameter is used by IDXREF
Maximum acceptable deviation (pixel units) between observed and calculated location of a diffraction peak. Reflections that do not satisfy this condition are excluded from the refinements.
Example: MAXIMUM_ERROR_OF_SPOT_POSITION=3.0
This is the default value for the parameter. The default value works
fine and hardly needs to be changed.
Parameter is used by IDXREF, INTEGRATE, CORRECT
Maximum acceptable deviation (degrees) between observed and calculated spindle angle of a diffraction peak. Reflections that do not satisfy this condition are not assigned indices and excluded from the subsequent refinements.
Example: MAXIMUM_ERROR_OF_SPINDLE_POSITION=2.0
This is the default value for the parameter. The default value works
fine and hardly needs to be changed.
Parameter is used by IDXREF, INTEGRATE, CORRECT
This parameter is a lower limit for the fraction of indexed spots compared to the total number of observed spots. The IDXREF step is considered successfully completed if more than the required minimum of spots are assigned indices.
Example: MINIMUM_FRACTION_OF_INDEXED_SPOTS=0.50
At least half of the given spots must be indexed (explained) by IDXREF.
This is the default value for the parameter. The default value works
fine and hardly needs to be changed.
Parameter is used by IDXREF
This parameter specifies which diffraction parameters are refined during
the IDXREF step. The parameter value can be ALL or any combination of the
KEYWORDS below in arbitrary order. ALL stands for all keywords except
SEGMENT.
The default value BEAM ORIENTATION CELL AXIS is assumed if the parameter is commented out. The direction of the rotation axis is not refined, however, if the diffraction spots given to IDXREF all come from a narrow rotation range (< 5°).
The keyword SEGMENT enables refinement of orientation and origin of each segment with respect to the detector system. For usual detectors consisting of a single segment the keyword is ignored. For a well calibrated detector it is usually better not to refine the segment parameters unless data from a truly calibration-grade crystal are being analysed.
To simplify configuration of the refinement protocol for detectors with many segments two additional parameters are used, namely MINIMUM_NUMBER_OF_REFLECTIONS/SEGMENT= and DEFAULT_REFINE_SEGMENT=. These two parameters are used to render all segments subject to refinement according to the keywords of the default refinement settings if at least a minimum number of reflections have been recorded by this segment - unless a private REFINE_SEGMENT= was explicitly specified. This overrides the default.
The refined diffraction parameters are saved in file XPARM.XDS.
Example 1: REFINE(IDXREF)=BEAM AXIS ORIENTATION CELL
This is the default and means that incident beam direction, rotation axis,
unit cell orientation and cell constants, but not the detector position,
will be refined during the IDXREF step.
Example 2:
REFINE(IDXREF)=BEAM AXIS ORIENTATION CELL POSITION SEGMENT
DEFAULT_REFINE_SEGMENT=POSITION ORIENTATION
MINIMUM_NUMBER_OF_REFLECTIONS/SEGMENT=200
Here, the refinement protocol consists of optimizing all parameter values
first except for the segment assembly parameters. In the final step
the refined values are fixed and only origin and orientation are
optimized for all segments that have registered at least 200 strong
reflections and are not explicitly specified to be treated differently.
Explicit control of the refined parameters for specified segments is provided
by the parameter REFINE_SEGMENT= along with
the definition of the detector segments in XDS.INP.
Parameter is used by IDXREF
This parameter specifies which diffraction parameters are refined during
the INTEGRATE step. Refinable diffraction parameters are named by keywords
Example 1: REFINE(INTEGRATE)= POSITION BEAM ORIENTATION CELL
This means that origin of the detector system, incident beam direction, unit
cell orientation and cell constants will be refined during the INTEGRATE step.
This is carried out in two steps with refinement of CELL constants only in
the last step while keeping the detector POSITION parameters constant. This
two-step procedure was adopted to bypass possible convergence problems of
the refinement procedure.
Example 2: REFINE(INTEGRATE)=!
The parameter is present in XDS.INP but does not specify any of the above keywords.
In this case the diffraction parameters are not refined during the INTEGRATE step
and remain as determined in IDXREF and saved in XPARM.XDS.
Parameter is used by INTEGRATE
The parameter value can be ALL (default) or any combination of the
following KEYWORDS in arbitrary order.
If the parameter is absent from XDS.INP or commented out or is specified as ALL, detector origin, beam direction, rotation axis, unit cell orientation, and cell constants will be refined in the CORRECT step of XDS. This is the default. The direction of the rotation axis is not refined, however, if the reflections in INTEGRATE.HKL all come from a narrow rotation range (< 5°).
The keyword SEGMENT enables refinement of orientation and origin of each segment with respect to the detector system. For usual detectors consisting of a single segment the keyword is ignored. For a well calibrated detector it is usually better not to refine the segment parameters unless data from a truly calibration-grade crystal are being analysed.
To simplify configuration of the refinement protocol for detectors with many segments two additional parameters are used, namely MINIMUM_NUMBER_OF_REFLECTIONS/SEGMENT= and DEFAULT_REFINE_SEGMENT=. These two parameters are used to render all segments subject to refinement according to the keywords of the default refinement settings if at least a minimum number of reflections have been recorded by this segment - unless a private REFINE_SEGMENT= was explicitly specified. This overrides the default.
Diffraction parameters not mentioned by their KEYWORDS remain fixed at the values provided in XDS.INP. (If a diffraction parameter meant to be fixed is not provided in XDS.INP, its values is taken from INTEGRATE.HKL.)
The refined diffraction parameters are saved in file GXPARM.XDS.
Example: REFINE(CORRECT)= BEAM ORIENTATION CELL
This means that incident beam direction, unit cell orientation and cell
constants, but not the detector origin nor the rotation axis, will
be refined in the CORRECT step. Detector origin and rotation axis will
remain as defined in XDS.INP.
Parameter is used by CORRECT
This parameter defines the default value of the parameter
REFINE_SEGMENT=.
Possible values can be DEFAULT_REFINE_SEGMENT= POSITION | ORIENTATION
If omitted, DEFAULT_REFINE_SEGMENT=! is assumed and segment refinements
will not be carried out unless explicitly requested by REFINE_SEGMENT=.
Example:
The example below shows the specification of 3 detector segments
and how their exact assembly with respect to the detector
system can be refined - assuming there are at least 300 observed spots
recorded by each segment.
segment 1 : refined parameter POSITION ORIENTATION, from default
segment 2 : refined parameter POSITION, explicitly requested
segment 3 : no parameter will be refined
MINIMUM_NUMBER_OF_REFLECTIONS/SEGMENT=300
DEFAULT_REFINE_SEGMENT=POSITION ORIENTATION
SEGMENT= 1483 1969 4453 4647
SEGMENT_ORGX= 1231.5
SEGMENT_ORGY= 4549.5
SEGMENT_DISTANCE= 250.0
DIRECTION_OF_SEGMENT_X-AXIS= 1.0000000 0.0000000 0.0000000
DIRECTION_OF_SEGMENT_Y-AXIS= 0.0000000 0.2246721 -0.9744344
SEGMENT= 1977 2463 4453 4647
REFINE_SEGMENT=POSITION!ORIENTATION
SEGMENT_ORGX= 1231.5
SEGMENT_ORGY= 4549.5
SEGMENT_DISTANCE= 250.0
DIRECTION_OF_SEGMENT_X-AXIS= 1.0000000 0.0000000 0.0000000
DIRECTION_OF_SEGMENT_Y-AXIS= 0.0000000 0.2246721 -0.9744344
SEGMENT= 1 487 4665 4859
REFINE_SEGMENT=!POSITION!ORIENTATION
SEGMENT_ORGX= 1231.5
SEGMENT_ORGY= 4761.5
SEGMENT_DISTANCE= 250.0
DIRECTION_OF_SEGMENT_X-AXIS= 1.0000000 0.0000000 0.0000000
DIRECTION_OF_SEGMENT_Y-AXIS= 0.0000000 0.0808889 -0.9967231
Parameter is used by IDXREF, CORRECT
The parameter specifies the minimum number of strong reflections recorded by a segment required for refinement of its position and orientation with respect to the detector instrument. Default value is 50.
Example: MINIMUM_NUMBER_OF_REFLECTIONS/SEGMENT=50
Segments containing less than 50 reflections are excluded from refinements
of their assembly parameters.
Parameter is used by IDXREF, CORRECT
This parameter defines sufficiently strong reflections that could be used for global refinement of geometrical parameters of the diffraction experiment.
Example: MINIMUM_I/SIGMA=3.0
Default value is 3.0. A smaller value would increase the number of reflections
used in the refinement. However, their centroids are less well defined.
Parameter is used by CORRECT
Angular life time (degrees) of a reflection to pass completely through the Ewald sphere on shortest route. The parameter value controls the raster size along gamma of the reflection profiles in step "INTEGRATE". A slightly larger value should be specified to include some background from adjacent data images.
If any of the parameters REFLECTING_RANGE=, REFLECTING_RANGE_E.S.D.=, BEAM_DIVERGENCE=, or BEAM_DIVERGENCE_E.S.D.= is left unspecified by the user, all these values will be determined automatically from the data images.
Example: REFLECTING_RANGE=0.80
It takes 0.8 degrees of rotation for a reflection to pass completely
through the Ewald sphere on shortest route.
Parameter is used by COLSPOT, IDXREF, INTEGRATE
Describes the mosaicity (degrees) of the crystal; that is the standard deviation of a Gaussian modeling the rocking curve.
If any of the parameters REFLECTING_RANGE=, REFLECTING_RANGE_E.S.D.=, BEAM_DIVERGENCE=, or BEAM_DIVERGENCE_E.S.D.= is left unspecified by the user, all these values will be determined automatically from the data images.
Example: REFLECTING_RANGE_E.S.D.=0.1
Mosaicity of the crystal is 0.1 degrees.
Parameter is used by INTEGRATE
This value is approximately arctan(spot diameter/DETECTOR_DISTANCE) and must be specified in degrees. A slightly larger value should be given to include some background pixels around each spot. To compute the spot diameter you need the pixel lengths (QX=, QY=) in mm which are listed in the Table of supported detectors. The parameter value defines the raster size along alpha/beta of the reflection profiles.
If any of the parameters REFLECTING_RANGE=, REFLECTING_RANGE_E.S.D.=, BEAM_DIVERGENCE=, or BEAM_DIVERGENCE_E.S.D.= is left unspecified by the user, all these values will be determined automatically from the data images.
Example: BEAM_DIVERGENCE=0.10
The value defines the solid angle of a diffraction spot in degrees.
Parameter is used by INTEGRATE
Defines the standard deviation of BEAM_DIVERGENCE=.
If any of the parameters REFLECTING_RANGE=, REFLECTING_RANGE_E.S.D.=, BEAM_DIVERGENCE=, or BEAM_DIVERGENCE_E.S.D.= is left unspecified by the user, all these values will be determined automatically from the data images.
Example: BEAM_DIVERGENCE_E.S.D.=0.025
Parameter is used by INTEGRATE
Defines the solid angle of a diffraction spot as multiple of its e.s.d. The default 5.0 is large enough to capture all intensity contributions plus some neighboring background region.
Example: RELRAD=6.0
The box representing reflection profiles contains more background
sampling points compared to the default 5.0.
Parameter is used by INTEGRATE
Defines the width of the rocking curve for reflections moving along the shortest route through the Ewald sphere as multiple of their mosaicity. The default 3.5 is large enough to capture all intensity contributions plus some background region from neighboring data images.
Example: RELBET=3.5
Parameter is used by INTEGRATE
These parameter values define the number of sampling points used for representing reflection profiles. Both values must be odd and positive numbers <22. Each reflection is mapped onto the surface of the Ewald sphere, the gamma-direction is along the shortest route when the reflection moves through the sphere (for details see Kabsch, 1988b).
Example: NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=9
NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=9
These are the default values. Each reflection when mapped to the surface
of the Ewald sphere is sampled by 9 x 9 raster points in the plane
tangential to the sphere and by 9 points along the shortest rotation route
through the sphere.
Parameter is used by INTEGRATE
Cut-off value defining the integration region in the learned reflection profiles. The size of the integration region is critical: Background noise will be added to the reflection intensities if this region is too large (decreasing CUT=); incomplete integration if the integration region is chosen too small (increasing CUT=).
Example: CUT=2.0
This is the default value. Grid points in the reflection profile less
than 2% of the maximum are not used for integration.
Parameter is used by INTEGRATE
This parameter allows to control the number of learned profiles
("INTEGRATE"). The number of profiles is approximately equal to
9 * Total rotation range covered by data set/DELPHI. If there are too
few strong spots which could be used for learning spot profiles, it may
be useful to specify a larger value for DELPHI=.
Example: DELPHI=5.0
The default value is 5 degrees of spindle rotation.
Parameter is used by INTEGRATE
Defines the minimum required percentage of observed reflection intensity. The missing intensity is estimated from the learned profiles. If less than MINPK % is observed, the reflection will be discarded.
Example: MINPK=75.0
The default value of 75% works fine and hardly needs to be changed.
Parameter is used by INTEGRATE, CORRECT
This parameter selects the integration method for reflection intensity. Profile fitting is used by default; alternatively integration can be carried out by straight summation.
Example: PROFILE_FITTING=TRUE
This is the default and usually results in better data than straight
summation could provide.
Parameter is used by INTEGRATE
This parameter controls the calculation of the absorption correction factors
in the CORRECT step of XDS. The parameter value can be TRUE or FALSE.
If STRICT_ABSORPTION_CORRECTION=FALSE (which is the default), Friedel-pairs
are temporaly treated as symmetry-equivalent reflections to impose additional
restraints during the calculation of the absorption correction factors. In the
presence of anomalous scattering effects this procedure could lead to a slight
underestimate of the anomalous differences - which is probably better
than to overestimate the anomalous effect.
If STRICT_ABSORPTION_CORRECTION= TRUE and
FRIEDEL'S_LAW=FALSE, Friedel-pairs
are treated as different reflections in the calculation of the absorption
correction factors. However, if FRIEDEL'S_LAW=TRUE, Friedel-pairs will
always considered symmetry-equivalent reflections in the determination
of the correction factors.
Example: STRICT_ABSORPTION_CORRECTION=TRUE
Note, that Friedel-pairs are treated as different reflections in the
calculation of the absorption correction factors only if
FRIEDEL'S_LAW=FALSE.
Parameter is used by CORRECT
The mean intensity of the reflections in the data set should not
correlate with the angular position of their diffraction maxima within
the rotation/oscillation range of the data images. The observed distribution
of the mean intensity is reported in CORRECT.LP. In some cases, deviations
from the expected uniform distribution may result from shutter problems
(suggested by Kay Diederichs).
The parameter PATCH_SHUTTER_PROBLEM= provides a way to patch this hardware
problem by an appropriate correction factor applied to the reflection
intensities. To apply this correction, specify PATCH_SHUTTER_PROBLEM=TRUE.
However, it is recommended to consult the person in charge of the beam-line
to find out whether such a hardware problem exists.
Example: PATCH_SHUTTER_PROBLEM=FALSE
This is the default, meaning that no such correction factors are applied
to the reflection intensities. The statistics is reported only.
Parameter is used by CORRECT
This parameter allows the user to select corrections to be applied to
the data. Possible values are a combination of the keywords
DECAY MODULATION ABSORPTION or ALL if all three corrections should be
carried out. Default value is CORRECTIONS= ALL.
DECAY indicates that correction factors should be determined and applied
to the intensities as function of image number and resolution.
MODULATION indicates that correction factors should be determined and applied
to the intensities as function of X and Y in the detector plane.
ABSORP indicates that correction factors should be determined and applied
to the intensities as function of image number and 13 reference positions
in the detector plane.
Example: CORRECTIONS=!
Here, no correction factors will be applied to the reflection intensities.
Parameter is used by CORRECT
This parameter defines the minimum required signal/noise of reflections used for determination of correction factors.
Example: SNRC=0.1
This is the default. A larger value would reduce the number of useful
reflections and lead to fewer correction factors that could be determined.
Parameter is used by CORRECT
Number of batches of consecutive images that make up the full data set. This number defines the sampling interval for correction factors along image number. To prevent overfitting, the parameter value should be chosen small enough so that there are enough strong, symmetry-related reflections. It is recommended to leave the parameter unspecified. In this case, XDS will determine a reasonable value.
Example: NBATCH=2
The data is covered by only 2 batches of images because of the low
symmetry of the crystal (say P1).
Parameter is used by CORRECT
This defines the angular range of rotation (°) covered by a batch of consecutive images. It is used to control the number of correction factors along image number.
Example: BATCHSIZE=5.0
A batch of consecutive images must cover 5.0° of spindle rotation.
This is the default.
Parameter is used by CORRECT
Defines the minimum number of reflections needed for the determination of each correction factor applied to the reflection intensities. The choice of a value for this parameter is strongly influenced by the crystal symmetry and the quality of its diffraction pattern. These crystal properties - together with the total rotation of the crystal during data collecting - define the number of reflection that can be used for the determination of the correction factors. Proper choice of a value for the parameter REFLECTIONS/CORRECTION_FACTOR= is a compromise between two considerations: A large value for this parameter leads to a small number of correction factors with low statistical errors; on the other hand, a small number of correction factors cannot model abrupt changes in the correction surface. The default value chosen by XDS is to use approximately 50 reflections for the determination of each correction factor.
Example: REFLECTIONS/CORRECTION_FACTOR=100
If your crystal has high symmetry and is well diffracting you may want to
use at least 100 reflections for each correction factor to reduce the
statistical error of the correction.
Parameter is used by CORRECT
You may specify here the file name of previously measured data from the
same crystal form. If available, these data are used by XPLAN and
CORRECT.
XPLAN uses the old data to tell the user by what strategy a maximum of
new data could be collected.
CORRECT uses the old data for local scaling and comparison with the
current data set. In case of setting ambiguities the reference data
are often used for selecting the best fitting one.
The reference data set is assumed to possess the symmetry specified by
the parameter SPACE_GROUP_NUMBER= in XDS.INP. As a consequence, for an
unknown space group, the reference data will be ignored.
The old, reference data set should be of type XDS_ASCII. If the data
cannot be read successfully, XDS assumes that there are no such data
available.
Example: REFERENCE_DATA_SET= ../XDS_ASCII_native.HKL
The file name of a reference data set.
Parameter is used by XPLAN, CORRECT
The reference data serve to check the consistency of indexing of the processed data, to recognize misindexing, to resolve possible ambiguities in the choice of the unit cell setting, and to adjust the isotropic resolution fall-off of the data to match that of the reference. The above input parameter allows to turn on or off B-factor matching with the reference data. The parameter can assume two values:
Example
REFERENCE_DATA_SET= ../XDS_ASCII_native.HKL
FIT_B-FACTOR_TO_REFERENCE_DATA_SET=FALSE
The reference data set named ../XDS_ASCII_native.HKL
is only used to check for correct indexing and unit cell choice
of the processed data set.
Parameter is used by CORRECT
This parameter influences the classification of outlier reflections in a list of symmetry related reflection intensities. For decision making the given standard errors obtained from the INTEGRATE step are multiplied by WFAC1. Thus, increasing values would result in fewer rejected reflections (MISFITS).
Example: WFAC1=1.5
Default value is 1.0 and hardly needs to be changed. A larger value,
like 1.5, would reduce the number of MISFITS (and increase the
R-factors).
Parameter is used by CORRECT
This parameter is used to mark extraordinarily strong reflections (by a negative standard deviation of its intensity) in the output file XDS_ASCII.HKL. Such "alien" reflections do not obey Wilson's statistic and often arise from ice rings in the data images. They are listed near the end in the file CORRECT.LP. "Aliens" with a Z-score above the parameter value are excluded from further processing.
Example: REJECT_ALIEN=20.0
"Aliens" with a Z-score above 20.0 are marked by a negative Sigma(I)
and are thus excluded from further processing (by XSCALE and XDSCONV).
This is the default value.
Parameter is used by CORRECT
This parameter is used to enforce identical scale factors for each data
image within a specified image range. This overrides the automatic
determination which could fail in principle for images with extremely low
background. Usually, the parameter is omitted because the automatic
determination works well in most cases.
The parameter has 3 numbers that specify first and last image number and
the value of the constant scale factor assigned to all images in the range.
An arbitrary number of such parameters can be specified in succession.
This parameter replaces the previous one, FIXED_SCALE_FACTOR=TRUE|FALSE.
Example: DATA_RANGE_FIXED_SCALE_FACTOR= 10 99 1.2
A fixed scale factor of 1.2 is used for data images 10 ... 99 in the data set.
Parameter is used by INIT, INTEGRATE
© 2009-2021, MPI for Medical Research, Heidelberg Imprint Datenschutzhinweis. Wolfgang.Kabsch@mpimf-heidelberg.mpg.de