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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).
 
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).
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== How does INTEGRATE treat overlaps? ==
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== How does INTEGRATE work? ==
    
The integration algorithm (see [http://dx.doi.org/10.1107/S0021889888007903]) proceeds along the following lines:
 
The integration algorithm (see [http://dx.doi.org/10.1107/S0021889888007903]) proceeds along the following lines:
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# pixel-labelling: the x,y,z, center of each pixel of the detector (z corresponds to phi, and the z pixelsize is delta-phi) is assigned to its closest (predicted) reflection in reciprocal space. As a consequence, ''each pixel of the detector is used for at most one reflection''.  
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# '''pixel-labelling''': the x,y,z, center of each pixel of the detector (z corresponds to phi, and the z pixelsize is delta-phi) is assigned to its closest (predicted) reflection in reciprocal space. As a consequence, ''each pixel of the detector is used for at most one reflection''.  
# transformation to local coordinate system: some of these pixels will mostly allow the background estimation, others will mostly contribute to the integration area (but there is not a 1:1 relationship).  
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# '''transformation to local coordinate system''': some of these pixels will mostly allow the background estimation, others will mostly contribute to the integration area (but there is not a 1:1 relationship).  
# 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).
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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).
# 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.
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# '''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 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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Among other things, this means that:
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Concerning overlap of reflections, this means that:
 
* there is ''no conceptual difference'' in XDS ''between overlap in x,y'' (due to too close detector, or smeared spots), ''and overlap by phi rotation'' (due to too large delta-phi, or high mosaicity).
 
* there is ''no conceptual difference'' in XDS ''between overlap in x,y'' (due to too close detector, or smeared spots), ''and overlap by phi rotation'' (due to too large delta-phi, or high mosaicity).
 
* the program does ''not'' look around each reflection to detect an overlap situation, it just gathers the pixels for each reflection.
 
* the program does ''not'' look around each reflection to detect an overlap situation, it just gathers the pixels for each reflection.
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