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INTEGRATE: Difference between revisions
→How does INTEGRATE treat overlaps?
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== How does INTEGRATE treat overlaps? == | == How does INTEGRATE treat overlaps? == | ||
The integration algorithm proceeds along the following lines: | |||
# the x,y,z, center of each pixel of the detector is assigned to its nearest (predicted) reflection in reciprocal space ("pixel-labelling", see [http://dx.doi.org/10.1107/S0021889888007903]). (The z coordinate corresponds to phi, and the z pixelsize is delta-phi.) | |||
# each pixel of the detector is assigned to its nearest reflection in reciprocal space ("pixel-labelling", see [http://dx.doi.org/10.1107/S0021889888007903]) | |||
# some of these pixels will mostly allow the background estimation, others will mostly contribute to the integration area (but as they are transformed into a local coordinate system [http://dx.doi.org/10.1107/S0021889888007903] there is not a 1:1 relationship). At this step, pixels which should be background but are higher than expected (due to overlap) are rejected. | # some of these pixels will mostly allow the background estimation, others will mostly contribute to the integration area (but as they are transformed into a local coordinate system [http://dx.doi.org/10.1107/S0021889888007903] there is not a 1:1 relationship). At this step, pixels which should be background but are higher than expected (due to overlap) are rejected. | ||
# for each reflection, the background is estimated, and the 3D profile is assembled from the pixels contributing to it | # for each reflection, the background is estimated, and the 3D profile is assembled from the pixels contributing to it | ||
# a comparison is made: for a reflection, is the percentage of its observed profile assembled in 3. larger than some constant (called "MINPK" in XDS.INP)? If the answer is no, this reflection will be discarded (too much "overlap"). | # a comparison is made: for a reflection, is the percentage of its observed profile assembled in 3. larger than some constant (called "MINPK" in XDS.INP)? If the answer is no, this reflection will be discarded (too much "overlap"). If the answer is yes, the observed intensity (from the incomplete profile) is scaled up with the inverse of the observed fraction (this relies on the accuracy of the average profile). | ||
Among other things, this means that: | Among other things, this means that: | ||
* there is no conceptual difference in XDS between overlap on a frame (due to too close detector, or smeared spots), and overlap by 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 tries to gather the pixels for each reflection | |||
* if two reflections differ in phi, but have the same position on the detector, then, as a consequence of 1. (above) the pixels are assigned to the reflection whose phi-calc is closest to the phi of the frame considered. (The relative intensities of these reflections are not taken into account because at this stage they are unknown!) | |||
* as a user, when your crystal-detector distance was chosen too low, or the reflections are very broad, or if the crystal has a high mosaicity (all of which result in many overlaps), you may try reducing MINPK down to some percentage between 75 and (say) 50. This will result in more completeness, but you should monitor the quality of the resulting data. Conversely, if you raise MINPK over its default of 75 you will discard more reflections, but the resulting dataset will be a bit cleaner. | |||