Hi Frank



I think this is a feature of (c)truncate - to avoid actually absent reflections messing up the French & Wilson correction for present-but-weak-or-negative reflections they are chucked out.



If you put data in e.g. P212121 into AIMLESS absent reflections will be written out. They only vanish when you make F’s.



Cheers Graeme



On 6 Apr 2018, at 08:11, Frank von Delft <[log in to unmask]<mailto:[log in to unmask]>> wrote:





Thanks James, that's a very useful steer - this is definitely an easy thing to get mixed up with, we can go scratch around there.



I now vaguely recall an ancient BB thread, where people were asking why the systematic absences get scrubbed out of the mtz files at all.  I must agree that I do not understand the rationale either:  the symmetry should be simply a label attached to the reflections, not something that wipes out potential observations.



(I'd be very happy to be wrong about this.)



Frank











On 06/04/2018 01:01, James Holton wrote:



I say "putative" because I don't know what your space group is.



In P212121 the reflection h,k,l = 0,0,1 is absent, but in P222 it is not absent.  So, if your unit cell is a=30 b=40 c=60 the lowest-angle hkl you will get is at 60 A resolution (0,0,1) in P222, but the lowest-angle reflection you will get out of P212121 will be (0,1,1), at 33.3 A resolution.  This is because 0,1,0 is also absent.  So, if you ever specify P212121 in your pipeline the 0,0,1 reflection will be lost.  Same thing happens with most any screw-vs-rotation axis assignment.



You loose other reflections to absences too, of course, but the lowest-order ones have an annoying habit of defining the "resolution range", and this can sometimes get set at one point in the pipeline and applied to subsequent operations, even if you change the space group back.  This could also be happening to you?



It is also possible to a subtle change in unit cell can move your lowest-order (and also the highest order) reflections across the defined "resolution range" boundaries.  Sometimes even round-off error can be enough.



So, if low-resolution is important it is always a good idea to replace the low-angle resolution limit with 9999 A.  Just be sure your beamstop was properly masked off.



-James Holton

MAD Scientist





On 4/5/2018 10:55 AM, Pearce, N.M. (Nick) wrote:

Could you expand a bit on what you mean by a “putative” systematic absence? (e.g. why only the lowest order hkl?)







On 5 Apr 2018, at 19:39, James Holton <[log in to unmask]<mailto:[log in to unmask]>> wrote:





You need to be careful with the exact space group at the particular stage in your pipeline here.  Often the lowest-order hkl is a putative systematic absence, so if you uniqueify in P222 you will get it, but if you uniqueify in P212121, then you won't.  That sort of thing.  Note that it doesn't matter what the "true" space group is, it only matters what is in the mtz header when you run uniqueify.



Could that be what is going on?



-James Holton



MAD Scisntist



On 4/5/2018 3:52 AM, Frank von Delft wrote:



Hello - can anybody shed light on this mystery:



We need (for PanDDA analysis) a lot of datasets each to have the complete set of low resolution indices, whether measured or not.  (Refmac adds the estimates as DFc, which is crucial when comparing maps.)



In ccp4, there are two obvious ways to get these indices complete:



  *   uniqueify

  *   CAD using the keyword "RESOLUTION FILE 1 999 <highres>"  (999 is the low resolution limit).



Mystifyingly, in ~1% of datasets, one or the other route misses one or two indices.  Our work-around is to go belt-and-braces and run both for each dataset.





It does however remain a bug.  Does anybody have any idea what's happening?  We can send example datasets to any volunteers who want to fiddle with it.



phx














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