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 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
