Low dose data: Difference between revisions

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The background counts per pixel are printed in INIT.LP, or can be estimated by visualizing the frames with [[XDS-Viewer]] or [[adxv]].
The average of the background counts per pixel are printed in INIT.LP, or can be estimated by visualizing the frames with [[XDS-Viewer]] or [[adxv]].


With the current version of XDS, the background of a data frame is used for scaling adjacent frames relative to each other in the INTEGRATE step.
In XDS, the background of a data frame is used for scaling adjacent frames relative to each other in the INTEGRATE step.


This seems to work very well down to an average of 0.5 counts/pixel. If, however, the crystal is exposed so shortly/weakly that the average drops significantly below this value, scaling becomes impossible - the ratio of averages which are around zero is obviously undefined. The keyword [http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#FIXED_SCALE_FACTOR= FIXED_SCALE_FACTOR] has been introduced to handle this situation.
This seems to work well down to an average of 0.05 counts/pixel. If, however, the crystal is exposed so shortly/weakly that the average drops significantly below this value, scaling becomes impossible - the ratio of averages which are around zero is obviously undefined. The keyword [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#DATA_RANGE_FIXED_SCALE_FACTOR== DATA_RANGE_FIXED_SCALE_FACTOR] has been introduced to handle this situation.
 
Another problem in this regime is that the background of a reflection is calculated from pixels around those that contribute to the reflection. If many of the background pixels are zero, the background becomes (relatively) less smooth, and empirically we find that the I/sigma values that XDS calculates may become overly optimistic. Whether use of [http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#FIXED_SCALE_FACTOR= FIXED_SCALE_FACTOR] mitigates this problem is not known yet.
 
It is therefore recommended that fine-slicing is performed according to the findings in the open-access paper [http://journals.iucr.org/d/issues/2012/01/00/wd5161/index.html] which means that the OSCILLATION_RANGE should be no less than half the REFLECTING_RANGE_E.S.D. ; choosing OSCILLATION_RANGE about the same as REFLECTING_RANGE_E.S.D. should result in data that are close to optimal.
 
Data frames which have been collected "too finely" may be added together using the [http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/merge2cbf_program.html merge2cbf] program of the XDS package.
 
All of this is currently only relevant for the Pilatus detector; a typical low background on other types of detectors is more on the order of 10 counts/pixel (Holton and Fraenkel (2010) Acta Cryst. (2010). D66, 393–408; [http://dx.doi.org/10.1107/S0907444910007262]).


See also: [[Difficult datasets]]
See also: [[Difficult datasets]]

Latest revision as of 11:28, 22 October 2019

The average of the background counts per pixel are printed in INIT.LP, or can be estimated by visualizing the frames with XDS-Viewer or adxv.

In XDS, the background of a data frame is used for scaling adjacent frames relative to each other in the INTEGRATE step.

This seems to work well down to an average of 0.05 counts/pixel. If, however, the crystal is exposed so shortly/weakly that the average drops significantly below this value, scaling becomes impossible - the ratio of averages which are around zero is obviously undefined. The keyword DATA_RANGE_FIXED_SCALE_FACTOR has been introduced to handle this situation.

See also: Difficult datasets

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