My immediate response to this is that anyone worrying about the number of reflections should get out more.
More seriously, is assessing the quality of measurements then multiple observed measurements of systematically absent reflections should agree within their error estimates and (ideally) have a mean = 0.0, thus it seems valid to include them in measures of internal consistency such as Rmerge, Rmeas (strictly they should be compared to 0 rather than their mean <Ih>), i suppose) On the other hand, in looking at intensity statistics (as in truncate) the observed intensities should be compared with their expectation values which will depend on the space group (but still included perhaps). However there are so few of these reflections that it won't make much difference (though it is more important to separate centric & acentric reflections, as there may be quite a lot of centrics) ie "situation normal" (SNAFU?) - it is not going to make any difference Phil On 24 Jan 2011, at 09:13, Graeme Winter wrote: > Dear ccp4bb, > > I had an interesting question from a xia2 user last week for which I > did not have a good answer. Here's the situation: > > - spacegroup is P212121, which was specified on the command-line > - xia2 processes this as oP, assigns the spacegroup as P212121 before > running scala -> generates merging stats > - truncate removes systematically absent reflections > > The end result is that there are fewer reflections in the output MTZ > file and hence used for refinement than are reported in the merging > statistics. The question is - what is correct? Clearly the effect on > the merging statistics will be modest or trivial as there were only ~ > 70 absent reflections, however removing them before scaling & merging > will also be a little fiddly. > > I see three (or maybe four) options - > > - truncate leave absent reflections in > - remove the absent reflections before scaling > - ignore this as "situation normal" (which is what xia2 currently does) > - (less helpful *) refine against intensities which includes the > absent reflections but matches the merging statistics > > If this were my project I would probably opt for #3 but I can > appreciate that this is a question for the wider audience. > > What do others think? > > Many thanks in advance, > > Graeme > > * I mark this as less helpful because this is the wrong *reason* to > merge against intensities. There are clearly good reasons for this.
