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Difficult datasets: Difference between revisions
→optimizing the parameters for COLSPOT
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These datasets have few (or few strong, or few well-defined) reflections per frame. Therefore, the multitude of parameters describing the diffraction experiment needs to be reduced (in refinement one would say: to avoid overfitting). This means that some parameters may need adjustment. | These datasets have few (or few strong, or few well-defined) reflections per frame. Therefore, the multitude of parameters describing the diffraction experiment needs to be reduced (in refinement one would say: to avoid overfitting). This means that some parameters may need adjustment. | ||
== optimizing the parameters for COLSPOT == | |||
play with the following [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html parameters], and use GNUPLOT (see below) to find their influence: | |||
STRONG_PIXEL= | |||
MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= | |||
It should be noted that it is important to correctly mask any shadowed areas on the detector; if not done properly, the variation at the edges will lead to spurious "spots" being picked up by COLSPOT. | |||
== optimizing the parameters for IDXREF == | == optimizing the parameters for IDXREF == | ||
Don't refine the DISTANCE in REFINE(IDXREF) ! | Don't refine the DISTANCE in REFINE(IDXREF) ! | ||
IDXREF depends on the reflection positions stored in SPOT.XDS . This file is written by COLSPOT, and its contents can be visualized e.g. with GNUPLOT: | |||
plot "SPOT.XDS" using 1:2 | |||
Obviously, only if the true reflection pattern is represented well by SPOT.XDS can IDXREF be successful. | |||
For close reflections, you may want to reduce SEPMIN below its default of 6, and set CLUSTER_RADIUS to half of the new value. | |||
== optimizing the parameters for INTEGRATE == | == optimizing the parameters for INTEGRATE == | ||