Hi Ed, I'm not directly familiar with the ctruncate implementation of French and Wilson, but from the implementation that I put into Phenix (based on the original F&W paper) I can tell you that any reflection where (I/sigI) - (sigI/mean_intensity) is less than a defined cutoff (in our case -4.0), then it is rejected. Depending on sigI and the mean intensity for a given shell, this can result in positive intensities that are also rejected. Typically this will effect very small positive intensities as you've observed.
I don't recall the mathematical justification for this and don't have a copy of F&W here at home, but I can have a look in the morning when I get into the lab and let you know. Jeff On Mon, Jun 17, 2013 at 5:04 PM, Ed Pozharski <epozh...@umaryland.edu>wrote: > I noticed something strange when processing a dataset with imosflm. The > final output ctruncate_etc.mtz, contains IMEAN and F columns, which > should be the conversion according to French&Wilson. Problem is that > IMEAN has no missing values (100% complete) while F has about 1500 > missing (~97% complete)! > > About half of the reflections that go missing are negative, but half are > positive. About 5x more negative intensities are successfully > converted. Most impacted are high resolution shells with weak signal, > so I am sure impact on "normal" refinement would be minimal. > > However, I am just puzzled why would ctruncate reject positive > intensities (or negative for that matter - I don't see any cutoff > described in the manual and the lowest I/sigI for successfully converted > reflection is -18). > > Is this a bug or feature? > > Cheers, > > Ed. > > -- > I don't know why the sacrifice thing didn't work. > Science behind it seemed so solid. > Julian, King of Lemurs >
