Changes

From XDSwiki
Jump to navigationJump to search
251 bytes added ,  11:14, 7 February 2011
Line 38: Line 38:  
# '''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.
+
# '''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:
Line 44: Line 44:  
* 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.
 
* if two reflections differ in phi, but have the same position on the detector, then, as a consequence of step 1 the pixels are assigned to that 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! Thus, ''no deconvolution is attempted''.
 
* if two reflections differ in phi, but have the same position on the detector, then, as a consequence of step 1 the pixels are assigned to that 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! Thus, ''no deconvolution is attempted''.
* 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 above its default of 75 you will discard more reflections, but the resulting dataset may be cleaner - again: ''check the statistics''.
+
* 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 (the default) and (say) 50. This will result in more completeness, ''but you should monitor the quality of the resulting data''. Conversely, if you raise MINPK above 75 you will discard more reflections, but the resulting dataset may be cleaner - again: ''check the statistics''. In particular, the latest versions of [[XDSSTAT]] prints out R_meas as a function of PEAK and intensity.
* this method degrades if the average profiles cannot be completey formed, as the scaling-up relies on their accuracy. This may happen if the reflections are too close in x,y and, at the same time, the mosaicity is high (such that no lunes exist, with edges that help constructing the average profiles). ''It is therefore useful to check the printed profiles in INTEGRATE.LP''.
+
* this method degrades if the average profiles cannot be completey formed, as the scaling-up relies on their accuracy. This may happen if the reflections are too close in x,y and, at the same time, the mosaicity is high (such that no lunes exist, with edges that help constructing the average profiles). ''It is therefore useful to check the printed profiles in INTEGRATE.LP''. Again, the latest versions of [[XDSSTAT]] help to find the best compromise between data quality and completeness.
Cookies help us deliver our services. By using our services, you agree to our use of cookies.

Navigation menu