nXDS: Files

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.

Information exchange between processing steps of nXDS
Files with the extension cbf are binary, compressed images.
nXDS step input files output files
XYCORR nXDS.INP XYCORR.LP
    X-CORRECTIONS.cbf
    Y-CORRECTIONS.cbf
FILTER nXDS.INP FILTER.LP
  image list image list (updated)
INIT nXDS.INP INIT.LP
  X-CORRECTIONS.cbf BKGINIT.cbf
  Y-CORRECTIONS.cbf BLANK.cbf
    GAIN.cbf
COLSPOT nXDS.INP COLSPOT.LP
  X-CORRECTIONS.cbf SPOT.nXDS
  Y-CORRECTIONS.cbf COLSPOT.LST
  BKGINIT.cbf  
POWDER nXDS.INP POWDER.LP
  SPOT.nXDS POWDER.cbf
IDXREF nXDS.INP IDXREF.LP
  SPOT.nXDS SPOT.nXDS
    XPARM.nXDS
INTEGRATE nXDS.INP INTEGRATE.LP
  X-CORRECTIONS.cbf INTEGRATE.HKL
  Y-CORRECTIONS.cbf  
  BLANK.cbf  
  BKGINIT.cbf  
  GAIN.cbf  
  XPARM.nXDS  
CORRECT nXDS.INP CORRECT.LP
  INTEGRATE.HKL nXDS_ASCII.HKL
    GXPARM.nXDS
    nXDS_long.HKL


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.


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.


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:


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

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.

The reflection records follow immediately after the !END_OF_HEADER line. A terminator record, !END_OF_DATA, follows the last reflection record.

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.


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Wolfgang.Kabsch@mpimf-heidelberg.mpg.de
page last updated: Dec 23, 2023