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 
<frank.vonde...@sgc.ox.ac.uk<mailto:frank.vonde...@sgc.ox.ac.uk>> 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 

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


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 
<jmhol...@slac.stanford.edu<mailto:jmhol...@slac.stanford.edu>> 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 

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.


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