Nonius logo KappaCCD User Manual 
 Revision 1.10, Last Update 1-July-1998

Integration

During integration the predicted spots on the images are integrated in two dimensions. Each integrated area represents a partial integrated reflection, since in general the reflection spot extends over more than one image.

The integration in the third dimension is done during scaling.

There is no further input required for the 2-dimensional integration. All parameters have been determined in the manual refinement part.

There are a few informative graphs displayed during integration.
The image display window is also updated every set of frames, depending on the setting of 3D window. It is useful to check whether the predictions are still covering the observed spots during the whole process.

Graphs of chi**2, cell axis size and axis orientations

In every batch of frames refinement of cell parameters is executed by default.
Some of the resulting refinement parameters are plotted in a graph against the frame number.
Graph of cell refinement chi**2 values against frame number
This plot tells you how well the predictions and observations are fitting in the X and Y direction of the frame. Good values are around 1.0. 
Larger values can be explained from spot shape distortion originating from crystal shape and special mosaicity effects. 
In general the values should be trendless. If the plot shows a trend it is worth checking what can be a plausible cause. 
 
  • Both X and Y show minimum and maximum values at the same frames, 180 degrees apart from each other.
    Most likely the cell symmetry is too high.
  • X values is always higher than Y values
    The (needle shaped) crystal is oriented along the rotation axis, resulting in a vertical spot shape
  • X and Y values cross over about every 90 degrees
    A plate shaped crystal is mounted along the rotation axes
 
Graph of cell refinement cell axis values against frame number
Graph of cell refinement axis orientation values against frame number
 

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