XDS Input Parameters

XDS: Input Parameters

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, the task of 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.

Table of supported detectors

For the MAR345, the number of detector pixels and their sizes are implied by the image file name extensions (like .mar2300 or .pck2300).

DETECTOR=	NX=	NY=	QX=	QY=	OVERLOAD=	Comments
ADSC	2304	2304	0.0816	0.0816	65000
MAR345	2300	2300	0.15	0.15	130000	.mar2300 or .pck2300
MAR345	2000	2000	0.15	0.15	130000	.mar2000 or .pck2000
MAR345	1600	1600	0.15	0.15	130000	.mar1600 or .pck1600
MAR345	1200	1200	0.15	0.15	130000	.mar1200 or .pck1200
MAR345	3450	3450	0.10	0.10	130000	.mar3450 or .pck3450
MAR345	3000	3000	0.10	0.10	130000	.mar3000 or .pck3000
MAR345	2400	2400	0.10	0.10	130000	.mar2400 or .pck2400
MAR345	1800	1800	0.10	0.10	130000	.mar1800 or .pck1800
MAR	1200	1200	0.15	0.15	130000
MAR	2000	2000	0.15	0.15	130000
MARCCD	2048	2048	0.064	0.064	65000
CCDDCHESS	1024	1024	0.0508	0.050	63000
RAXIS	950	950	0.2034	0.210	250000	RAXIS-II
RAXIS	1900	1900	0.1017	0.105	250000	RAXIS-II
RAXIS	3000	3000	0.100	0.100	250000	RAXIS-IV
RAXIS	4000	4000	0.100	0.100	250000	RAXIS-V
MAC	2500	2500	0.08	0.08	250000	DIP2020
MAC	3000	3000	0.10	0.10	250000	DIP2030
SMARTCCD	1024	1024	0.089	0.089	250000
CCDD2AM	1242	1152	0.191	0.191	65000
ESRF	1242	1152	0.1298	0.129	65000
VIDEMETRIX	512	512	0.1369	0.136	4095
CCDBRANDEIS	1024	1024	0.1000	0.100	42000
SIEMENS	512	512	0.19	0.19	65000

JOB=

The value of JOB= can be ALL (default) or any combination of the keywords described below. Each keyword names a subroutine to be executed.

XYCORR: computes a table of spatial correction values for each pixel
INIT: determines an inital background for each detector pixel and finds the trusted region of the detector surface.
COLSPOT: collects strong diffraction spots from a specified subset of the data images
IDXREF: interprets observed spots by a crystal lattice and refines all diffraction parameters.
DEFPIX: defines the trusted region of the detector, recognizes and removes shaded areas, and eliminates regions outside the resolution range defined by the user.
XPLAN: helps planning data collection. Typically, one or a few data images are collected initially and processed by XDS. XPLAN reports the completeness of data that could be expected for various starting angles and total crystal rotation. Warning: If data were initially processed for a crystal with unknown cell constants and space group, the reported results will refer to space group P1.
INTEGRATE: collects 3-dimensional profiles of all reflections occuring in the data images and estimates their intensities
CORRECT: corrects intensities for decay, absorption and variations of detector surface sensitivity, reports statistics of the collected data set and refines the diffraction parameters using all observed spots.

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.

MAXIMUM_NUMBER_OF_PROCESSORS=

This parameter defines the maximum number of cpu's that can be employed by the parallel version of XDS for data processing. Up to 32 cpu's can be handled. The default of 1 cpu will be assumed in the single processor version of XDS. Also, if the parameter MINUTE= is greater than zero, only one processor will be used.

Example: MAXIMUM_NUMBER_OF_PROCESSORS= 16

MINUTE=

Maximum number of minutes for XDS to wait until data image must appear (default is 0).

Example: MINUTE=60
This allows you to start data processing by XDS while data collection is still going on, but note that only one processor will be used.

Parameter is used by XYCORR, INIT, COLSPOT, INTEGRATE.

TEST=

Test flag for additional diagnostics and control images.

0 : turns off additional checks;
1 : default. Generates the control image FRAME.pck
2 : additional diagnostics like overloaded pixels are provided

Parameter is used by XYCORR, INIT, COLSPOT, INTEGRATE.

DETECTOR=

Specifies the detector used for data collection. The parameter value can be:

ADSC
ADSC Q4, Q105, Q210, Q315 CCD-detectors, SMV image Format
MAR345
new marresearch (X-ray Research) imaging plate detector
MAR
old marresearch (X-ray Research) imaging plate detector
CCDCHESS
CCD-detector at CHESS and MAR CCD-detector at BROOKHAVEN
RAXIS
R-AXISII, R-AXISIV, or R-AXISV imaging plate detector
MAC
MacScience imaging plate detector, ENRAF NONIUS DIP-series
SMARTCCD
CCD-detector BRUKER SMART-series
CCDD2AM
CCD-detector at ESRF Grenoble (beamline D2AM)
ESRF
CCD-detector at ESRF Grenoble (beamline 3)
VIDEMETRIX
CCD-detector at Brandeis (designed by Walter Phillips)
CCDBRANDEIS
CCD-detector at Brandeis (1024 X 1024) and Brookhaven
SIEMENS
Siemens/Nicolet multiwire detector

Example: DETECTOR=CCDCHESS
If the MAR CCD or the CCD detector at CHESS was used for data collection.

Parameter is used by XYCORR, INTEGRATE

NX=
NY=

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

QX=
QY=

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

OVERLOAD=

Maximum valid contents of an image pixel. The number of overloaded pixels in each image are reported only, except for the "CORRECT" step. Here, overloaded reflections are excluded from the final output. Consult Table of supported detectors for selection of an appropriate parameter value or use the default value (which is detector dependent) by omitting this parameter altogether.

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 XYCORR, INIT, COLSPOT, INTEGRATE, CORRECT

MINIMUM_VALID_PIXEL_VALUE=

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.

Parameter is used by INIT, COLSPOT, INTEGRATE

RMAX=

Relative radius limiting the trusted region on the detector. A pixel at IX, IY is marked untrusted in the INIT step of XDS if ((IX-NX/2)/(NX/2))**2 + ((IY-NY/2)/(NY/2))**2 > RMAX**2. Default is 1.0. This parameter provides a simple way of defining the acceptable detector surface.

Example: RMAX=1.35
This includes the corners of the rectangular detector for data collection.

Parameter is used by INIT

ROFF=
TOFF=

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

BRASS_PLATE_IMAGE=

File name, access, and format of brass-plate image used in step XYCORR to calculate the spatial correction tables X-CORRECTIONS.pck and Y-CORRECTIONS.pck. This is mandatory for the SIEMENS, BRUKER, and CCDD2AM detectors. 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= ../../calibration/grid_002 ESRF DIRECT

Parameter is used by XYCORR

HOLE_DISTANCE=

Grid distance (mm) between brass-plate holes. If specified, the given value overrides the default settings for SIEMENS, BRUKER, or CCDD2AM detectors. 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

MXHOLE=

Number of calibration holes of the brass-plate. If specified, the given value overrides the default settings for SIEMENS, BRUKER, or CCDD2AM detectors. 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

MNHOLE=

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 SIEMENS, BRUKER, or CCDD2AM detectors. 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

DARK_CURRENT_IMAGE=

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.pck". The parameter is optional. If a dark-current image is not available, the table "BLANK.pck" is generated either from the value of the parameter OFFSET= or -in case of the CCDD2AM detector- from the mean value at the four corners of a data image. 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

OFFSET=

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.pck" is generated by "INIT" either from the value of the parameter OFFSET= or -in case of the CCDD2AM detector- from the mean value at the four corners of a few data images.

Parameter is used by INIT

VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=

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.pck from the initial background table BKGINIT.pck (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.pck and removed from the trusted detector region. The table BKGPIX.pck should always be inspected with the VIEW program to see whether the excluded detector region makes sense. If you observe that some shaded regions are still included in BKGPIX.pck, 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

INCLUDE_RESOLUTION_RANGE=

An accepted reflection h, k, l must have a resolution d(h,k,l)=lambda/{2sin(theta)} within the specified 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.pck. To verify that the chosen resolution range is appropriate you should always visually check BKGPIX.pck with the VIEW program (type VIEW BKGPIX.pck).

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 DEFPIX, CORRECT

EXCLUDE_RESOLUTION_RANGE=

Resolution range (Å) for excluding reflections. This feature allows to remove ice-rings from the final data (unfortunately also good reflections in the specified resolution range). From 0, which is the default, up to 10 such ranges may be specified. 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.

Parameter is used by CORRECT

NAME_TEMPLATE_OF_DATA_FRAMES=

Generic file name, format, and access mode of data images.

Example:
NAME_TEMPLATE_OF_DATA_FRAMES= ../mckhg_???.image MAR DIRECT

For accessing a specific data image, XDS will substitute the appropriate image number for the question marks in the generic file name template. Compressed versions (using the UNIX compress, gzip, or bzip2 routines) of the data image files are automatically recognized by XDS. The file name extensions (.Z, .z, .gz, bz2) due to the compression routines should not be included in the generic file name template. As the full length of file names is restricted by XDS to at most 50 characters, lengthy path names (i.e. images residing on a different computer) should be abbreviated by a symbolic link using the UNIX command:

ln -s long_path_name_image_directory Images

The name template may be followed by keywords specifying format and access mode of the data image files. Unfortunately, for each detector there exists at least one different format for recording an image. XDS assumes a default format for each detector type. However, the user has the option to specify a different format, for example CCP4, if the data images have been previously converted by Jan Pieter Abrahams compression algorithm using the program 2pck.
The format KEYWORD can be:

HARVARD: SIEMENS multiwire detector
ARGONNE: SIEMENS multiwire detector
MAR: marresearch-detector
MAR345: New MAR345 image format
RAXIS: R-AXISII, R-AXISIV, or R-AXISV detector
MAC: MacScience (ENRAF NONIUS) imaging plate detector for both 12-bit (DIP2020) and 16-bit (DIP2030)
VIDEMETRIX: CCD-detector designed by Walter Phillips
CCDD2AM: CCD-detector at ESRF Grenoble
ESRF: Format of another CCD-detector at ESRF
CCP4: Compressed images by Jan Pieter Abrahams algorithm with number representation used at MRC
TIFF: TIFF-format used by CCDCHESS and MARCCD detectors
CCDBRANDEIS: CCD-detector (1024 X 1024) at Brandeis & Brookhaven
BRUKER: Bruker area detector image data format (old and new SMART6000)
SMV: ADSC CCD-detector image data format

The format keyword applies to all data images with the given generic file name template. The optional keywords DIRECT or SEQUENTIAL (at most one of these two) specify the images as random access (DIRECT) or sequential unformatted (SEQUENTIAL) files.

A more efficient compression routine for images has been designed by Jan Pieter Abrahams. XDS handles images with the number representation used at the MRC as well as MAR images compressed by the new algorithm. The latter type of images are recognized by the file name extension .pck (instead of .image) in NAME_TEMPLATE_OF_DATA_FRAMES=.

Parameter is used by INIT, COLSPOT, IDXREF, INTEGRATE

DATA_RANGE=

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

BACKGROUND_RANGE=

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 degrees starting with the first data image collected.

Example: BACKGROUND_RANGE= 2 6
The initial background table BKGINIT.pck will be determined from the data images 2, 3, ..., 6.

Parameter is used by INIT

SPOT_RANGE=

Numbers of the first and last data image used for finding strong spots. Up to 10 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 MINUTE=>0 then SPOT_RANGE=BACKGROUND_RANGE else SPOT_RANGE=DATA_RANGE

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. If the crystal has not slipt 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.

Parameter is used by COLSPOT

PROFILE_RANGE=

This parameter specifies a range of image numbers. These images are used for automatic determination of the diffraction peak profile parameters REFLECTING_RANGE=, BEAM_DIVERGENCE=, and their E.S.D.'s. Up to 10 such ranges may be specified. If no PROFILE_RANGE= parameter value is specified, the same data images as specified by the SPOT_RANGE= parameter(s) are used by default. Automatic determination will not be attempted if all of the peak profile parameters REFLECTING_RANGE=, REFLECTING_RANGE_E.S.D.=, BEAM_DIVERGENCE=, and BEAM_DIVERGENCE_E.S.D.= are specified by the user.

Example:
PROFILE_RANGE= 2 10
PROFILE_RANGE=32 41
PROFILE_RANGE=50 50
Images 2 to 10, 32 to 41, and image 50 will be used for automatic determination of the diffraction peak profile parameters, overriding the default.

Parameter is used by INTEGRATE

ORGX=
ORGY=

These two parameters denote the X- and Y-coordinates (pixels) of the detector origin. The origin is defined as that point on the detector which is closest to the crystal (the intersection point between the incident beam and the rotation axis).
Note, that the origin differs from the position of the incident beam on the detector, if the beam is not exactly normal to the detector. No default values are provided by XDS as the origin depends on the detector alignment and the type of the detector. The user should pay attention to specify sufficiently correct parameter values as an incorrect choice could easily lead to misindexing of the reflections!

Example: ORGX= 605.0 ORGY= 592.0 NX=1200 NY=1200
If the incident beam is approximately normal to the detector and hits the detector at the center of the instrument, the origin is near NX/2, NY/2.

Parameters are used by XYCORR, IDXREF

DETECTOR_DISTANCE=

Signed distance of the detector from the crystal (mm). The sign depends on the direction of the detector normal, which is specific to the detector type, and for this reason the parameter value could come out negative ! XDS provides no default for the magnitude of the parameter. However, if you use the XDS.INP template appropriate for your detector, the sample parameter value provided has the correct sign.

Example: DETECTOR_DISTANCE= 330.1
The detector is at a distance of 330.1 mm with the detector normal pointing away from the crystal.

Parameter is used by IDXREF

DIRECTION_OF_DETECTOR_X-AXIS=
DIRECTION_OF_DETECTOR_Y-AXIS=

These two orthonormal vectors define a matrix ED which describes the orientation of the detector with respect to the laboratory coordinate system.
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)
The third unit vector, the detector normal, is then defined as ED(.,3)=ED(.,1) X ED(.,2) to make a right-handed orthonormal system. The detector orientation matrix ED is needed to map the pixel coordinates on the detector to the laboratory coordinate system. A pixel at IX,IY on the detector 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)
Here, QX, QY are the lengths of a pixel (mm) along X and Y, respectively. ORGX, ORGY are the pixel coordinates of the origin, and DETECTOR_DISTANCE=F is the signed detector distance (mm). It may well be that a negative F has to be chosen since the sign of F depends on the direction of the detector normal !

Default parameter values 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. A general procedure to find out how a pixel at address IX+NX*(IY-1) in the data image is mapped to the laboratory coordinate system is described in the section COORDINATE SYSTEMS.

Example:
DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
The "fast" pixels run along the laboratory x-axis and the "slow" pixels along the laboratory y-axis. The detector normal then points along the laboratory z-axis. The parameter DETECTOR_DISTANCE= would be negative if the detector normal points towards the crystal.

Parameters are used by IDXREF

ROTATION_AXIS=

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=

Oscillation range of each data image in degrees (>0). 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.

Example: OSCILLATION_RANGE=0.1
This describes a "fine-sliced" data set with each image covering an oscillation range of 0.1 degrees.

Parameter is used by IDXREF

X-RAY_WAVELENGTH=

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

INCIDENT_BEAM_DIRECTION=

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=

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.

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

POLARIZATION_PLANE_NORMAL=

x, y, z components of the polarization plane normal with respect to the laboratory coordinate system.

For an unpolarized beam hitting the crystal:
FRACTION_OF_POLARIZATION=0.5
POLARIZATION_PLANE_NORMAL= an arbitrary vector

For a monochromator with incident unpolarized beam:
FRACTION_OF_POLARIZATION=[cos(2*thetaM)]**2/[1+(cos(2*thetaM))**2]
POLARIZATION_PLANE_NORMAL= components of the monochromator diffraction plane normal.

Example:
POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0
FRACTION_OF_POLARIZATION=0.9
The electrical field vector of the incident beam is found in the x,z-plane of the laboratory coordinate system with a probability of 0.9.

Parameter is used by CORRECT

AIR=

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 degrees.

Example: AIR=0.001
This is the default value.

Parameter is used by CORRECT

SPACE_GROUP_NUMBER=

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_CONSTANTS=

Unit cell parameters a, b, c (Å) and alpha, beta, gamma (degrees). 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 degrees as required by the space group.

Parameter is used by IDXREF, CORRECT

REIDX=

Optional transformation providing a possibility of reindexing the reflections in the CORRECT step. The meaning of the 12 integer numbers that make up the parameter is defined as:
h' = REIDX(1)*h + REIDX( 2)*k + REIDX( 3)*l + REIDX( 4)
k' = REIDX(5)*h + REIDX( 6)*k + REIDX( 7)*l + REIDX( 8)
l' = REIDX(9)*h + REIDX(10)*k + REIDX(11)*l + REIDX(12)
where h', k', l' are the new indices.
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 IDXREF.LP.

Example 1: REIDX= 1 0 0 0 0 1 0 0 0 0 1 0
This transformation yields h'=h, k'=k, l'=l, which puts the new indices equal to the original indices h, k, l. This is the default assumed if this transformation is omitted or the space group is unknown.

Example 2
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. Suggestions for possible space groups are listed in IDXREF.LP together with the required reindexing transformation and new cell constants. To test the hypothesis that the crystal belongs to the tetragonal space group P4₂(#77), the user only has to change the 4 parameters by the values given above and to rerun the last step of XDS. 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

FRIEDEL'S_LAW=

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.

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

STARTING_ANGLE=
STARTING_FRAME=

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

STARTING_ANGLES_OF_SPINDLE_ROTATION=

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 degrees. 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

TOTAL_SPINDLE_ROTATION_RANGES=

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_SHELLS=

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

REFERENCE_DATA_SET=

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.
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

NBX=
NBY=

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.pck. 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

BACKGROUND_PIXEL=

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

STRONG_PIXEL=

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

MAXIMUM_NUMBER_OF_STRONG_PIXELS=

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

MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=

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

SPOT_MAXIMUM-CENTROID=

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=2.0
This is the default value for the parameter.

Parameter is used by COLSPOT

SIGNAL_PIXEL=

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

INDEX_ORIGIN=

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

INDEX_ERROR=

Maximum allowed deviation from 'integerness' of computed indices of a reflection. This parameter corresponds to epsilon in reference 1.

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

INDEX_MAGNITUDE=

Maximum magnitude of index differences between reflections. This parameter corresponds to delta in reference 1.

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

INDEX_QUALITY=

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 (reference 1). 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

SEPMIN=

Minimum distance (pixels) between diffraction spots considered when looking for difference vector clusters.

Example: SEPMIN=6.0
This is the default value for the parameter. The default value works fine and hardly needs to be changed.

Parameter is used by IDXREF

CLUSTER_RADIUS=

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
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_ERROR_OF_SPOT_POSITION=

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

REFINE(IDXREF)=

The parameter value can be ALL (default) or any combination of the following KEYWORDS in arbitrary order.

DISTANCE - refine detector distance
BEAM - refine direct beam direction
AXIS - refine rotation axis
ORIENTATION - refine unit cell orientation
CELL - refine unit cell orientation and cell constants

If ALL is specified or the parameter is commented out, detector distance, beam direction, rotation axis, unit cell orientation, and cell constants will be refined in the IDXREF step of XDS. The direction of the rotation axis is not refined, however, if the diffraction spots given to IDXREF all come from a narrow rotation range (less than 5 degrees).

If no parameter value is specified, XDS assumes either REFINE(IDXREF)=ORIENTATION (if space group and cell constants are known) or REFINE(IDXREF)=ORIENTATION CELL (for an unknown crystal). All other parameters remain fixed.

The refined diffraction parameters are saved in file XPARM.XDS.

Example: REFINE(IDXREF)=BEAM AXIS ORIENTATION CELL
This means that incident beam direction, rotation axis, unit cell orientation and cell constants, but not the detector distance, will be refined during the IDXREF step.

Parameter is used by IDXREF

REFINE(INTEGRATE)=

The parameter value can be ALL or any combination of the following KEYWORDS in arbitrary order.

DISTANCE - refine detector distance
BEAM - refine direct beam direction
AXIS - refine rotation axis
ORIENTATION - refine unit cell orientation
CELL - refine unit cell orientation and cell constants

If ALL is specified, detector distance, beam direction, rotation axis, unit cell orientation, and cell constants will be refined in the INTEGRATE step of XDS. The direction of the rotation axis is not refined, however, if the diffraction spots given to the refinement routine all come from a narrow rotation range (less than 5 degrees). This is usually the case since the spots are taken from a small batch of images. Consequently, the default parameter value is REFINE(INTEGRATE)=DISTANCE BEAM ORIENTATION CELL

If none of the above KEYWORDS is given, the diffraction parameters are not refined during the INTEGRATE step and remain as determined in IDXREF and saved in XPARM.XDS.

Example: REFINE(INTEGRATE)= BEAM CELL
This means that incident beam direction, unit cell orientation and cell constants, but not the detector distance nor the rotation axis, will be refined during the INTEGRATE step.

Parameter is used by INTEGRATE

REFINE(CORRECT)=

The parameter value can be ALL or any combination of the following KEYWORDS in arbitrary order.

DISTANCE - refine detector distance
BEAM - refine direct beam direction
AXIS - refine rotation axis
ORIENTATION - refine unit cell orientation
CELL - refine unit cell orientation and cell constants

If ALL is specified, detector distance, beam direction, rotation axis, unit cell orientation, and cell constants will be refined in the CORRECT step of XDS. This is the default assumed if the parameter REFINE(CORRECT)= is omitted (or commented out) from XDS.INP. The direction of the rotation axis is not refined, however, if the reflections in INTEGRATE.HKL all come from a narrow rotation range (less than 5 degrees).

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 CELL
This means that incident beam direction, unit cell orientation and cell constants, but not the detector distance nor the rotation axis, will be refined in the CORRECT step. Detector distance and rotation axis will remain as defined in XDS.INP.

Parameter is used by CORRECT

REFLECTING_RANGE=

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 specified by the PROFILE_RANGE= parameters. Default is to omit specification of the parameter value.

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

REFLECTING_RANGE_E.S.D.=

Describes the mosaicity (degrees) of the crystal; that is the standard deviation of a Gaussian modeling the rocking curve.

Example: REFLECTING_RANGE_E.S.D.=0.1
Mosaicity of the crystal is 0.1 degrees.

Parameter is used by INTEGRATE

BEAM_DIVERGENCE=

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.

Example: BEAM_DIVERGENCE=0.10
The value defines the solid angle of a diffraction spot in degrees.

Parameter is used by INTEGRATE

BEAM_DIVERGENCE_E.S.D.=

Defines the standard deviation of BEAM_DIVERGENCE=.

Example: BEAM_DIVERGENCE_E.S.D.=0.025

Parameter is used by INTEGRATE

NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=
NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=

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 reference 2). XDS will determine the parameter values unless specified by the user.

Example: NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=9
NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=9
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=

Cut-off value defining the integration region in the learned reflection profiles.

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

DELPHI=

This parameter allows to control the number of learned profiles ("INTEGRATE") and scaling factors ("CORRECT"). 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, CORRECT

MINPK=

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 CORRECT

WFAC1=

This parameter is used for recognizing MISFITS (reflections that are incompatible with the observed intensities of symmetry related ones).

Example: WFAC1=1.5
Default value is 1.5 and hardly needs to be changed. A smaller value like 1.0 would increase the number of MISFITS (and reduce the R-factors).

Parameter is used by CORRECT

STRICT_ABSORPTION_CORRECTION=

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, Friedel-pairs are treated as symmetry-equivalent reflections in the calculation of the absorption correction factors. In the presence of anomalous scattering effects this could lead to an underestimate of the anomalous differences.
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.

Example: STRICT_ABSORPTION_CORRECTION=TRUE
This is the default. 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

PATCH_SHUTTER_PROBLEM=

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

Wolfgang Kabsch
page last updated: September 15, 2003

XDS Input Parameters

XDS: Input Parameters

Job control

Detector hardware

Detector distortions

Detector noise

Trusted detector region

Data images

Detector position

Rotation axis

Incident beam

Crystal

Background and peak pixels

Indexing and refinement

Peak profiles

Correction factors