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The spot size and shape and the size of the background box can be determined in the "Integration Box" area.
The profile fitting radius (see the HKL manual) determines how many reflections will be used for profile fitting. This can be easily seen with the display program. Click the button "Prof fit R". Attached to the mouse you will now have a circle. Also, the number of predicted reflections will decrease, depending on the value of "Refinement Sigma Cutoff" and all reflections you see are above the sigma threshold. For every reflection to be processed, the profile will be calculated based on those that are within the circle defined by "Profile Fitting Radius" and are above the sigma cutoff level. It is therefore important to take the radius not too small, e.g. 15, and the sigma cutoff level not too high (e.g. 3 - 5), otherwise there will be no reflections present to apply the profile fitting for the weak reflections.
The `Box size' and `Spot size' determine the integration and background area. Make sure that the spot size is big enough to surround a reflection and that the number of pixels in the box, outside the outer circle is roughly equal to the number of pixels within the inner circle. The box and spot circles can be shown in the zoom window of the display level, by clicking "Zoom wind". Middle clicking a reflection in the main window will centre on that reflection and pressing "Zoom in" will zoom in on the reflection. Pressing "Int Box" will show the integration box.
A new feature has been added that corrects for skew incidence at theta=0. This is the Elongation limit option. If you tick this box, the predicted spots will get an elongated shape after another refinement run. Obviously this effect is most pronounced at high resolution as can be seen below:
More options of the box size can be explored by clicking : Options, Level, "Advanced". Here one can manually change the size and shape of the box and the inner and outer circle of the spot. This may be useful in the case of very elongated spots, where one would like to make the box and circle oblong instead of square.
If one would take parameters as in the following window:
one would get boxes and spot areas as below.
