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33 bytes added ,  15:03, 3 March 2008
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# '''average profile''': the average profile is formed on a grid (using the 3D local coordinate system) from strong reflections. The signal part of the profile is defined by those gridpoints of the average profile that are above a threshold (called "CUT" in XDS.INP).
 
# '''average profile''': the average profile is formed on a grid (using the 3D local coordinate system) from strong reflections. The signal part of the profile is defined by those gridpoints of the average profile that are above a threshold (called "CUT" in XDS.INP).
 
# '''estimating the intensity''': for each reflection, the background is estimated, and the 3D profile is assembled from the pixels contributing to it. Pixels which are mostly background but whose counts are higher than expected (e.g. due to overlap) are rejected.
 
# '''estimating the intensity''': for each reflection, the background is estimated, and the 3D profile is assembled from the pixels contributing to it. Pixels which are mostly background but whose counts are higher than expected (e.g. due to overlap) are rejected.
# '''handling overlap''': not all pixels of a reflection, which would be required to assemble its full profile (whose shape is given by the average profile), may have been observed due to step 1. Therefore, in another pass, for each reflection, the observed fraction of its theoretical profile is calculated. If this fraction is less than a threshold (called "MINPK" in XDS.INP), this reflection will be discarded ("too much overlap"). If it is above MINPK, the observed intensity (from the incomplete profile) is scaled up with the inverse of the fraction.
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# '''handling overlap''': not all pixels of a reflection, which would be required to assemble its full profile (whose shape is given by the average profile), may have been observed due to step 1. Therefore, in another pass, for each reflection, the observed fraction of its theoretical profile is calculated. If this fraction (column "PEAK" in XDS_ASCII.HKL) is less than a threshold (called "MINPK" in XDS.INP), this reflection will be discarded ("too much overlap"). If it is above MINPK, the observed intensity (from the incomplete profile) is scaled up with the inverse of the fraction.
    
Concerning overlap of reflections, this means that:
 
Concerning overlap of reflections, this means that:
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