If we have not overload cutoff value in the command file what does it decide as the overload value when printing the statistics after each image?
Default value is OK for R-axis and some MAR scanners. It represents the full dynamic range of possible numbers in the file. Now Denzo reads overload table from MAR scanners. On some old MAR scanners spiral to Cartesian conversion program incorrectly handled saturation. Newer version seem to be OK. Some sites may have locally modified software (EMBL-Hamburg, MRC Cambridge), check with whoever made the modification. With MAR scanners user has to know instrument he or she is using.
When looking at the Denzo output I noticed that some reflections are flagged with backgr ovfl. This seems to be independent from the parameters of background elliptical or spot elliptical or overload value. Are there other parameters controlling this backgr ovfl ?
The backgr ovfl flag may be set a an overloaded pixel, but also by a high percentage of pixels rejected from background calculation. On MAR scanners spots outside active area (corners of the image) will never have valid background and will have backgr ovfl condition set.
backgr ovfl column is really sum of all reflections with any kind of problem with background, one of the possibilities being having one or more overflowed pixels in the background areas. Other problems are background varying too much, or too many pixels being obscured by other reflections, or too many pixels not having a valid measurements. The last affects mostly spots outside active area of the detector. Adjusting resolution limits can prevent prediction of spots there. overload value has only effect on one of the factors involved.
When you say outlier rejection - what exactly do you mean? I tried changing overload value to 40000, but it doesn't make much difference. Should error systematic be increased then? I integrated with it at 5.0 - should I try with 10.0 say?
Neither overload value nor error systematic have any direct impact on outlier rejection. overload value defines detector saturation. Systematic error in Denzo is a number that describes expected correlation between positional errors on the detector. Outlier rejection happens when symmetry related reflections do not agree in measured intensity.
What exactly is the scanner doing to give such funny data?
Another problem with MAR scanners is sometimes a wrong scale factor applied to strong fluorescence signal compared to weak signal. Setting overload value to below transition point between strong and weak range of data may help, but this would eliminate a lot of reflections. Transition point is roughly at about 10000 MAR units.
'show overloads' does not work with most file formats.
It works now with all formats.