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 is that below 0.5 counts/pixel, the I/sigma values become overly optimistic. Whether this is due to the intensities being too high or the sigmas too low has not yet been investigated; likely it's the latter. This effect is ''not'' mitigated by use of [http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#FIXED_SCALE_FACTOR= FIXED_SCALE_FACTOR] .
 
CC1/2 (printed out in CORRECT.LP since version of March 15, 2012), on the other hand, appears to be more realistic.
 
It is therefore recommended that
* exposure time and flux is high enough to ensure at least 0.5 counts per pixel, on average.
* 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/weakly 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 12:28, 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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