[phenixbb] Reflection file woes phenix/ccp4/PDB

[Nathaniel Echols]

On Fri, Dec 16, 2011 at 6:50 AM, Machius, Mischa Christian
<mischa_machius at med.unc.edu> wrote:
> Yes, the thought that the anomalous R free flags could have something to do with it occurred to me as well, so I checked. As far as I can see, the test reflections are evenly distributed between the + and - sets; they were not selected from the + or - set only. For the vast majority of the test reflections, both Bijvoet mates were measured and both were flagged properly. For some, however, only one Bijvoet mate was measured and flagged. It probably wouldn't do any harm to consolidate the test flags, discarding the few with only one measured Bijvoet mate, but I really don't see why it should be necessary to do so.

It shouldn't - many/most of those missing Bijvoet mates may simply be
centric reflections.  The fact that the completeness shows up as
significantly less than 100% is (in my opinion) a bug somewhere either
in the MTZ library or our wrapper for it, because I've seen this even
in files with synthetic, 100% complete anomalous data.  You should be
able to consolidate the test flags, but you don't need to discard any.

-Nat