General

nXSCALE combines the results of processing several streams of snapshots (file type INTEGRATE.HKL) into a single file (type nXDS_ASCII.HKL) containing fully corrected integrated intensities in a format as obtained from the general rotation data processing program XDS. The file is thus ready for use by subsequent program packages for structure determination. Note, that the case of a single stream of snapshots is already handled by the CORRECT step of nXDS and does not require running nXSCALE.

nXSCALE assumes that all streams of snapshot images

• are from crystals of the same compound, space-group symmetry and unit cell metric
• are recorded by the same detector.

The program allows that for each stream of snapshots

• the detector could be at different locations and orientations with altered geometrical arrangement of its segments (in case of a multi-segment instrument)
• direction, wavelength and polarization of the incident beam could differ
• rotation axis and oscillation range could vary (mixing of streams of 'stills' and rotation images is allowed)

Preparation of processing by nXSCALE begins by copying an input file template nXSCALE.INP into the data processing directory and subsequent editing to provide the correct parameter values for the actual scaling/post-refinement run. All possible input parameters are listed in nXSCALE: Input parameters.

Results from running the program are collected in the ASCII file nXSCALE.LP in the processing directory. This file should always be studied carefully as it reports the statistics of the quality of the final data set and also diagnostics in case of problems.

The parameter values obtained after post-refinement are saved in ASCII files GXPARM_#.nXDS with # enumerating the input streams of snapshots.

Details

The operation of nXSCALE is best explained using an Example for nXSCALE.INP (see below). A classical rotation data set (OSCILLATION_RANGE=0.1) was collected by a pixel detector (PILATUS 12M) consisting of 120 segments arranged in a cylindrical way.

The output file obtained from running nXSCALE is named nXSCALE-test.HKL

The 3600 images were previously processed by nXDS as 4 separate streams of snapshots. The files (relative to the nXSCALE processing directory)
../nXDS_2-1001/INTEGRATE.HKL
../nXDS_1002-2000/INTEGRATE.HKL
../nXDS_2001-3000/INTEGRATE.HKL
../nXDS_3001-3600/INTEGRATE.HKL
resulting from the INTEGRATE step carried out in their private processing directories serve as input files in our nXSCALE example.

Except for the polarization parameters (FRACTION_OF_POLARIZATION=0.99 POLARIZATION_PLANE_NORMAL=0 1 0) all other parameters describing the diffraction experiment and the detector (location and internal segment arrangements) are taken from the header of the input files. Knowledge of the polarization is not required for integration and therefore absent from the file header. It is only needed for calculating intensity correction factors in the nXSCALE or CORRECT step (see below).

In principle, the artificial splitting of the images into 4 streams was not necessary because oscillation range, rotation axis, beam direction and polarization, as well as detector location and orientation were identical. However, for large data sets it is advisable to evaluate the data in smaller pieces and gather the compatible ones using nXSCALE.

In case a fairly complete data set from crystals of the same compound, space-group symmetry and unit cell metric is available it could serve as a useful reference to resolve setting ambiguities and to pinpoint misindexed snapshots. In our example such a data set is indeed available because the 3600 images could also be processed as a classical rotation data set by XDS,
REFERENCE_DATA_SET=../XDS_Auswertung/XDS_ASCII.HKL

The integrated intensities of the reflections of the input files may or may not have been indexed in the correct space-group. For the purpose of integration it is only important that all reflections occurring in the data images have been accurately located and indexed with respect to some unit cell basis. The reflection indices in the correct space-group are always a linear transformation of the original indices used in the INTEGRATE step.
Presently, nXSCALE / CORRECT requires knowledge of the space-group and approximate cell constants. Plausible space-group candidates and their conventional cell parameters were already reported in IDXREF.LP and can now be tried in the nXSCALE / CORRECT step without the need for rerunning previous program steps. In our example we know from processing with XDS:
SPACE_GROUP_NUMBER=230 UNIT_CELL_CONSTANTS= 50.97 50.97 50.97 90 90 90

Criteria for rejecting snapshots are based on excessive deviations in their beam directions from the median direction found for each input stream. The accepted images are then reindexed according to the given conventional cell and all possible reindexing transformations are memorized. The median of the cell parameters after reindexing is determined for all images from all input streams. Recognition and removal of outliers among the images is based on decision parameters
MAX_CELL_AXIS_ERROR=0.03 ! 3% deviation from median value of axis
MAX_CELL_ANGLE_ERROR=3.0 ! 3° deviation from median value of angle

Reflections from the input files are accepted that are

• not overloaded, defined by OVERLOAD=1048500
• within resolution range, defined by INCLUDE_RESOLUTION_RANGE=999.9 0.70
• recorded sufficiently close to the calculated Bragg peak, defined by MINIMUM_EWALD_OFFSET_CORRECTION=0.7

Intensity correction factors must be calculated for each accepted reflection. Some of these factors depend on material constants of the detector and air absorption which are valid for all input streams of snapshots. Knowledge of the sensor material (SILICON=35.0) and its thickness (SENSOR_THICKNESS=0.32) is needed to correct intensities due to differences in path lengths of the diffracted beams. In our example there is no air absorption (AIR=0.0) because sample and detector are in vacuum. As mentioned above corrections due to polarization of the incident beam are specified separately for each input stream as they could depend on specific details of the diffraction experiment in the general case.

Post-refinement improves the final data set by changes of the crystallographic parameters of all images so that intensities of symmetry equivalent reflections become as similar as possible to each other and simultaneously minimize discrepacies between calculated and observed spot positions on the detector segments. In the example, all possible parameters except B-FACTOR and MOSAICITY are optimized by post-refinement,
POSTREFINE= POSITION BEAM ORIENTATION CELL SEGMENT! B-FACTOR MOSAICITY
For each input stream translation and rotation of all of the 120 segments with respect to the detector coordinate system should be refined by default,
DEFAULT_REFINE_SEGMENT= POSITION ORIENTATION
with the exception of the segment specified by
SEGMENT= 1 487 1 195 REFINE_SEGMENT=! POSITION ORIENTATION
which should remain fixed. (Note that the exclamation mark turns the qualifier POSITION ORIENTATION into comments.) Clearly, for a meaningful refinement of the segment parameters a minimum number of observed spots should have been recorded,
MINIMUM_NUMBER_OF_REFLECTIONS/SEGMENT=200
Since an excellent reference data set is available from processing the identical set of images as a conventional rotation data set by XDS it is used for the intensity part of the post-refinement target function
USE_REFERENCE_IN_POSTREFINEMENT=TRUE ! FALSE is default

!============= Data sets for scaling & post-refinement
OUTPUT_FILE=nXSCALE-test.HKL
 INPUT_FILE=../nXDS_2-1001/INTEGRATE.HKL
  FRACTION_OF_POLARIZATION=0.99  POLARIZATION_PLANE_NORMAL=0 1 0
 INPUT_FILE=../nXDS_1002-2000/INTEGRATE.HKL>
  FRACTION_OF_POLARIZATION=0.99  POLARIZATION_PLANE_NORMAL=0 1 0
 INPUT_FILE=../nXDS_2001-3000/INTEGRATE.HKL
  FRACTION_OF_POLARIZATION=0.99  POLARIZATION_PLANE_NORMAL=0 1 0
 INPUT_FILE=../nXDS_3001-3600/INTEGRATE.HKL>
  FRACTION_OF_POLARIZATION=0.99  POLARIZATION_PLANE_NORMAL=0 1 0
REFERENCE_DATA_SET=../XDS_Auswertung/XDS_ASCII.HKL
     
!============= Crystal
SPACE_GROUP_NUMBER=230
UNIT_CELL_CONSTANTS= 50.97  50.97  50.97   90  90  90
     
!============= Criteria for accepting images
!MAX_CELL_AXIS_ERROR=0.03
!MAX_CELL_ANGLE_ERROR=3.0

!============= Criteria for accepting reflections
OVERLOAD=1048500
INCLUDE_RESOLUTION_RANGE=999.9 0.70
MINIMUM_EWALD_OFFSET_CORRECTION==0.7
!REJECT_ALIEN==20.0

!============= Intensity correction factors
AIR=0.0
!SILICON==35.0
SENSOR_THICKNESS==0.32

!============= Post-refinement
POSTREFINE= POSITION BEAM ORIENTATION CELL SEGMENT! B-FACTOR MOSAICITY
DEFAULT_REFINE_SEGMENT= POSITION ORIENTATION
MINIMUM_NUMBER_OF_REFLECTIONS/SEGMENT=200
!SEGMENT= 1 487   1 195   REFINE_SEGMENT=! POSITION ORIENTATION
USE_REFERENCE_IN_POSTREFINEMENT=TRUE ! FALSE is default