INTEGRATE

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This article is under construction!

INTEGRATE is the most important step ("JOB") of XDS. This steps writes the logfile INTEGRATE.LP. Its task is (for each reflection)

  1. to calculate the frame(s) where it contributes, and the pixel positions
  2. to integrate, using profile-fitting, the observed pixel contents
  3. to write the observed intensities, their standard deviations, their positions and a number of less important data to INTEGRATE.HKL

While it does this, it also refines all geometrical parameters of the diffraction experiment.

Some explanations of definitions given by Wolfgang Kabsch (slightly edited)

  • Observed spot coordinates
  1. A pixel is defined 'strong' if its contents is above the mean plus a certain number (say, 3) estimated standard deviations of the surrounding background pixel values.
  2. Two 'strong' pixels belong to the same spot if they are found adjacent in 3 dimensions; like x,y,z :: x+1,y,z :: x,y,z+1 :: etc.
  3. A spot is defined as the set of all 'strong' pixels being adjacent, directly or indirectly.
  4. Observed spot coordinates are defined as centroid of the 'strong' pixels (after background subtraction) and spatial corrections available from the X,Y-lookup tables are added to the centroids.

This definition covers the case that a spot may extend over many images or just appears on a single image. Note that XDS uses z-centroids instead of phi-angles about the spindle axis. This definition allows for bimodal spot shapes as well.

Note that this means that for weak reflections there are no observed spot coordinates.

  • Calculated spot coordinates

These are the x,y,z coordinates of the centroid of Gaussians (i.e. unimodal) centered at the ideal Bragg peak x,y,phi using initial guesses for the variances (which are later replaced by estimates using the observed images).

The mapping of each pixel to the Ewald sphere uses a local, reflection specific coordinate system the origin of which corresponding to the ideal Bragg peak x,y,phi. This is used for profile fitting and has nothing to do with the definitions of observed and calculated spot coordinates.

XDS does not adjust the integration boxes such as to center them individually on the observed reflections: it only tries to minimize the deviations between observed and calculated spot coordinates by adjusting about a dozen diffraction parameters (those given by REFINE(INTEGRATE)) for the reflections in a certain range of frames (DELPHI).