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INTEGRATE: Difference between revisions
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→Some explanations of definitions given by Wolfgang Kabsch (slightly edited)
(New page: '''This article is under construction!''' INTEGRATE is the most important step ("JOB") of XDS. This steps writes the logfile INTEGRATE.LP. Its task is (for each reflection) # to calcu...) |
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# A pixel is defined 'strong' if its contents is above the mean plus a certain number (say, 3) estimated standard deviations of the surrounding background pixel values. | # A pixel is defined 'strong' if its contents is above the mean plus a certain number (say, 3) estimated standard deviations of the surrounding background pixel values. | ||
# Two 'strong' pixels belong to the same spot if they are found adjacent in 3 dimensions; like x,y,z :: x+1,y,z :: x,y,z+1 :: etc. | # Two 'strong' pixels belong to the same spot if they are found adjacent in 3 dimensions; like x,y,z :: x+1,y,z :: x,y,z+1 :: etc. | ||
# A spot is defined as the set of all 'strong' pixels being adjacent, directly or indirectly | # A spot is defined as the set of all 'strong' pixels being adjacent, directly or indirectly. | ||
# Observed spot coordinates are defined as centroid of the 'strong' pixels (after background subtraction) and spatial corrections available from the X,Y-lookup tables are added to the centroids. | # Observed spot coordinates are defined as centroid of the 'strong' pixels (after background subtraction) and spatial corrections available from the X,Y-lookup tables are added to the centroids. | ||
This definition covers the case that a spot may extend over many images or just appears on a single image. Note that XDS uses z-centroids instead of phi-angles about the spindle axis. This definition allows for bimodal spot shapes as well. | This definition covers the case that a spot may extend over many images or just appears on a single image. Note that XDS uses z-centroids instead of phi-angles about the spindle axis. This definition allows for bimodal spot shapes as well. | ||
Note that this means that for weak reflections there are no observed spot coordinates. | |||
* Calculated spot coordinates | * Calculated spot coordinates | ||
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The mapping of each pixel to the Ewald sphere uses a local, reflection specific coordinate system the origin of which corresponding to the ideal Bragg peak x,y,phi. This is used for profile fitting and has nothing to do with the definitions of observed and calculated spot coordinates. | The mapping of each pixel to the Ewald sphere uses a local, reflection specific coordinate system the origin of which corresponding to the ideal Bragg peak x,y,phi. This is used for profile fitting and has nothing to do with the definitions of observed and calculated spot coordinates. | ||
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 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). | ||