The files generated by nXDS are either ASCII type files that can be inspected and modified by using a text editor, or binary, compressed image files that can be looked at using the XDS-Viewer program.

All files have a fixed name defined by nXDS, which makes it mandatory to process each data set in a newly created directory to avoid name clashes. Clearly, one should not run more than one nXDS-job simultaneously in the same directory.

The data images are processed in 8 steps which are executed in succession by nXDS. Results and diagnostics from each step are documented in files with the name extension .LP for inspection by the user. Information between the steps is exchanged by files, which allows repetition of selected steps with a different set of input parameters without rerunning the whole program. Note, that by rerunning a processing step the earlier version of the output files from this step will be overwritten. Thus, these older files should first be given another name if their original contents are meant to be saved.

nXDS.INP

This file contains the input parameters you have to specify to run nXDS.

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 parameter value must directly follow the parameter name and be on the same line. The parameter names cannot be abbreviated; they are case sensitive, too. The parameters may be given in arbitrary order. Characters in a line to the right of an exclamation mark are comment.

nXDS_ASCII.HKL

This file contains the result of data processing by nXDS, namely the corrected intensities of all reflections recorded by the data images. This file can be directly read by XDSCONV which is part of the ( XDS). program package. XDSCONV also converts the reflection data from nXDS_ASCII.HKL into various formats required by software packages for crystal structure determination like CCP4, CNS (X-PLOR), or SHELX.

nXDS_ASCII.HKL consists of a header, reflection data records, and a line marking the end of the data. Each line is at most 530 characters in length. The data records consist of a fixed number of numerical items that are separated by at least one blank. Header lines and the terminator line are distinguished from the reflection data records by the presence of the exclamation mark symbol '!' as first character.

• Header
  The first header line defines the file format (always FORMAT=XDS_ASCII), states that symmetry equivalent reflections have not been merged (always MERGE=FALSE), and Friedel's law does not hold (always FRIEDEL'S_LAW=FALSE).
  Subsequent header lines specify experimental parameter values and other information whose meaning is obvious or refers to an input parameter value explained in the section Input parameters. The amount of information given in the header may vary and is subject to future development. However, the header always specifies the number of numerical items in each reflection data record, which is the value of the parameter called NUMBER_OF_ITEMS_IN_EACH_DATA_RECORD=.
  Each reflection data record contains 5 items whose meanings are specified by the following keywords.
  • ITEM_H=1; the first number in a data record is the reflection index h.
  • ITEM_K=2; the second number in a data record is the reflection index k.
  • ITEM_L=3; the third number in a data record is the reflection index l.
  • ITEM_IOBS=4; the fourth number in a data record is the reflection intensity. It is corrected for various effects like Lorentz, polarization, Ewald-offset, and oblique incidence of the diffracted beam on the detector. Item 4 is essentially the squared structure factor amplitude.
  • ITEM_SIGMA(IOBS)=5; the fifth number is the error of the corrected intensity (item 4).
  The last line of the header is identified by !END_OF_HEADER
• Data records
  For each unique reflection and its Friedel mate (if available), weighted averages of intensities and sigmas from two equally-sized groups of randomly selected snapshots are provided (at most 4 lines/unique reflection). The meaning of the data items in each line is explained in the header. Each data record line consists of numerical items which are separated by at least one blank. The chosen way of presenting the final results of data processing by nXDS could greatly reduce the length of the output file - yet providing all necessary information to use anomalous effects.
• Terminator record
  !END_OF_DATA

nXDS_long.HKL

This stands for the name of an optional reflection output file which contains the result of data processing by nXDS in detail, namely the corrected intensities of all reflections recorded in the data images. The file could become potentially very large and is therefore generated only if explicitly requested by the user. This is done by specifying a non-blank file name for the input parameter in nXDS.INP, like for example LONG_OUTPUT_FILE=nXDS_long.HKL
The name was chosen in the example to avoid name clashes with other files generated by this processing. This file can be directly read by XDSCONV which is part of the ( XDS). program package. XDSCONV converts the reflection data from nXDS into various formats required by software packages for crystal structure determination like CCP4, CNS (X-PLOR), or SHELX.

The LONG_OUTPUT_FILE consists of a header, reflection data records, and a line marking the end of the data. Each line is at most 530 characters in length. The data records consist of a fixed number of numerical items that are separated by at least one blank. Header lines and the terminator line are distinguished from the reflection data records by the presence of the exclamation mark symbol '!' as first character.

• Header
  The first header line defines the file format (always FORMAT=XDS_ASCII), states that symmetry equivalent reflections have not been merged (MERGE=FALSE), and that Friedel's law does not hold true (FRIEDEL'S_LAW=FALSE).
  Subsequent header lines specify experimental parameter values and other information whose meaning is obvious or refers to an input parameter value explained in the section Input parameters. The amount of information given in the header may vary and is subject to future development. However, the header always specifies the number of numerical items in each reflection data record, which is the value of the parameter called NUMBER_OF_ITEMS_IN_EACH_DATA_RECORD=10.
  Each reflection data record contains 10 items whose meanings are specified by the following keywords.
  • ITEM_H=1; the first number in a data record is the reflection index h.
  • ITEM_K=2; the second number in a data record is the reflection index k.
  • ITEM_L=3; the third number in a data record is the reflection index l.
  • ITEM_IOBS=4; the fourth number in a data record is the reflection intensity. It is corrected for various effects like Lorentz, polarization, Ewald-offset, and oblique incidence of the diffracted beam on the detector. Item 4 is essentially the squared structure factor amplitude.
  • ITEM_SIGMA(IOBS)=5; the fifth number is the error of the corrected intensity (item 4). A negative sign is attached to indicate a MISFIT; i.e. the intensity (item 4) is incompatible with symmetry equivalent reflection intensities. At present, such MISFITs are ignored in the subsequent processing by xscale.
  • ITEM_XD=6; calculated X-coordinate (pixels) of reflection on detector.
  • ITEM_YD=7; calculated Y-coordinate (pixels) of reflection on detector.
  • ITEM_Q=8; is the correction factor for the various effects applied to the raw, integrated intensity recorded in the snapshot to yield the final intensity reported by item 4.
  • ITEM_INF=9; denotes the running number of the INPUT_FILE containing the reflection data. All of the input files included in the scaling are enumerated together with their file names in the header of this long output file.
  • ITEM_IMG=10; specifies the running number of the image within this INPUT_FILE. These numbers and their associated image file names are provided in the header of the INPUT_FILE (type INTEGRATE.HKL).
  The last line of the header is identified by !END_OF_HEADER
• Data records
  one line per reflection, with the meaning of the data items in each line being explained in the header. Each data record line consists of numerical items which are separated by at least one blank. A negative sign is attached to SIGMA(IOBS) to indicate a MISFIT.
• Terminator record
  !END_OF_DATA

SPOT.nXDS

The first line is the path name of the directory containing the images. Now, for each image accepted by "COLSPOT", the following structure is repeated:

• First line is the file name of the image.
• Second line consists of three integers reporting the number of background pixels, strong pixels, and accepted spots, respectively.
• Third and following lines each report info for one accepted spot; #,x,y,I,h,k,l
  where # is ident number of the detector segment where the spot is recorded, x,y are coordinates (pixel) of spot centroid after correction for spatial distortions, and I is sum of values of the strong pixels belonging to the spot. h,k,l are the reflection indices attached by the subsequent "IDXREF" step. Indices 0 0 0 are used to indicate a spot that could not be indexed.

COLSPOT.LST

Each line contains the file name of a data image with a sufficient number of diffraction spots that might be worthwhile to analyze by subsequent steps.

XPARM.nXDS

This file contains a header part and a body that provides for each successfully indexed data image all necessary information for computing the Bragg peaks of reflections expected to occur in the image. These parameters are determined by "IDXREF" and used by "INTEGRATE".

Header contains general information valid for all images

• first line specifies path name of the directory containing the images
• second line contains 6 numbers that specify
  1. number of accepted images,
  2. number of detector segments,
  3. number of pixels along X (fast direction) of image,
  4. number of pixels along Y (slow direction) of image,
  5. size of a fast pixel (mm),
  6. size of a slow pixel (mm)
• third line contains the space group number
• the fourth line of the header specifies oscillation range of each image (0 for stills) and
  direction cosines of the rotation axis with respect to the laboratory coordinate system (0 0 0 for stills)
• beginning with the fifth line each detector segment is specified by one line containing
  1. x1,x2,y1,y2 defining all pixels x,y belonging to this segment as x1 ≤ x ≤ x2 and y1 ≤ y ≤ y2
  2. segment X-coordinate (pixel) of origin wrt detector system
  3. segment Y-coordinate (pixel) of origin wrt detector system
  4. segment distance (mm) from origin of the detector system
  5. coordinates of segment X-axis wrt detector system
  6. coordinates of segment Y-axis wrt detector system

Body part of the file provides the following 9 lines of information for each image

1. File name of the image
2. Wavelength (Å) and laboratory coordinates of the incident beam wavevector
3. Laboratory coordinates of the unit cell a-axis (Å)
4. Laboratory coordinates of the unit cell b-axis (Å)
5. Laboratory coordinates of the unit cell c-axis (Å)
6. Origin (pixels) and signed distance (mm) of the detector coordinate system
7. Laboratory coordinates of the detector system X-axis
8. Laboratory coordinates of the detector system Y-axis
9. Laboratory coordinates of the detector system Z-axis

GXPARM.nXDS

This file contains the parameters obtained from the postrefinement replacing the corresponding ones of file XPARM.nXDS. This offers a possibility to rerun the INTEGRATE and CORRECT steps after replacement of XPARM.nXDS by the new file, hopefully improving results.

POWDER.cbf

This control image is generated by the POWDER step of nXDS. The image shows a powder pattern generated from the spots from all images. Inspecting the resulting image with the XDS-Viewer could be helpful for specifying the laboratory coordinates of the incident beam direction.

INTEGRATE.HKL

This file contains the results from the INTEGRATE step. The file begins with a self-explaining header. Each header record line starts with a '!'. The last header record is indicated by !END_OF_HEADER. The header contains 3 blocks of information about each image.

• IMAGE_NAMES enumerates the successfully integrated images and provides the file name corresponding to each enumerated image.
• DIFFRACTION_PARAMETERS provides for each image one line of information: Image number, wavelength (Å), incident_beam wavevector (1/Å), basis_vectors{a,b,c} (Å), detector_origin {ORGX,ORGY(pixels),F(mm)}.
• IMAGE_CONTROL provides for each image one line of information: Image number, number of reflections, number of background_pixels, number of spot pixels, number of strong_spots, number of superimposed spot profiles, number of overloaded reflections, and six values of the profile parameters that were actually used for integration:
  BEAM_DIVERGENCE=, 3 parameters sigma1,sigma2,rho describing the shape of the reflections after mapping to the Ewald sphere as a bivariate normal distribution, and a number pair for the parameter REFLECTING_RANGE_E.S.D.= sigmaR1 sigmaR2. The e.s.d. of the reflecting range is a linear function, sigmaR1 + p * sigmaR2, of the length p (1/Å) of the reciprocal lattice point. A Gaussian with the above e.s.d. is used to model the decline of reflection intensity with distance of the reciprocal lattice point from the Ewald sphere in a resolution dependent way.

Each reflection record consists of 14 numerical data items
h,k,l,ISEG,MAXC,IOBS,SIGMA,POBS,XOBS,YOBS,XCAL,YCAL,Q,Image#
that are output as a single line not longer than 180 characters. The numerical items are separated by a blank and can be read in free-format.

1. h: h-index of the reflection.
2. k: k-index of the reflection.
3. l: l-index of the reflection.
4. ISEG: ident number of the segment where the spot is recorded.
5. MAXC: largest image pixel value contributing to the reflection.
6. IOBS: intensity of the reflection obtained by profile fitting. IOBS is already corrected for a missing fraction due to intruding neighbours or untrusted pixels.
7. SIGMA: e.s.d. of IOBS as obtained from profile fitting.
8. POBS: percentage of observed reflection intensity estimated by comparison with a reference profile.
9. XOBS: observed detector X-coordinate of the reflection. 0 if unobserved.
10. YOBS: observed detector Y-coordinate of the reflection. 0 if unobserved.
11. XCAL: calculated detector X-coordinate of the reflection.
12. YCAL: calculated detector Y-coordinate of the reflection.
13. Q: correction factor acccounting for Ewald offset, Lorentz- and polarization, air absorption and sensor thickness effects. IOBS/Q and SIGMA/Q are estimates for the 'true', fully corrected intensity and its e.s.d. except for a scaling/temperature factor and possible reindexing.
14. Image#: identifying number of the snapshot image containing this reflection

X-CORRECTIONS.cbf
Y-CORRECTIONS.cbf

The files X-CORRECTIONS.cbf and Y-CORRECTIONS.cbf are generated by the XYCORR step of nXDS and contain look-up tables to correct the X and Y pixel positions on the detector for spatial distortions. The spatial corrections for a pixel at IX,IY (1≤IX≤NX, 1≤IY≤NY) are found in the tables at address IA4=IX4+NXBY4*(IY4-1) where IX4=1+(IX-2)/4, IY4=1+(IY-2)/4, and NXBY4= 1+(NX-2)/4, such that the corrected pixel-coordinates are
IX("CORRECTED")=IX+I2XCOR(IA4)/10
IY("CORRECTED")=IY+I2YCOR(IA4)/10.
The files can be visualized using the XDS-Viewer program. The spatial corrections reported by clicking the left mouse button are in pixel units multiplied by 10.

BLANK.cbf

BLANK.cbf contains the dark current (non-Xray) background. The dark current for a pixel at IX,IY (1≤IX≤NX, 1≤IY≤NY) is found at position IA=IX+NX*(IY-1) in the expanded file.

GAIN.cbf

GAIN.cbf contains the ratio between variance and mean of the pixel contents in the neighbourhood of each image pixel. The values are multiplied by 1000 and rounded to the nearest integer. They are saved for a pixel at IX,IY (1≤IX≤NX, 1≤IY≤NY) at position IA=IX+NX*(IY-1) in the expanded file.

BKGINIT.cbf

This file contain an image of the INTEGER array IBKG(NX*NY) such that IBKG(IX+NX*(IY-1)) is the background value at pixel position IX,IY (1≤IX≤NX, 1≤IY≤NY). NX,NY are the number of pixels along the detector X- and Y-axis. (IX is the fast index.)

BKGINIT.cbf is generated in the INIT step and should be inspected by the user with the xds-viewer to recognize shaded regions of the detector. These pixel regions on the detector can be specified using the input parameters UNTRUSTED_RECTANGLE=, UNTRUSTED_ELLIPSE=, and UNTRUSTED_QUADRILATERAL= followed by rerunning the INIT step. Untrusted pixels are marked by -3.