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.
