Hi,
Looking at the pointless logfile for P222, there’s excellent evidence for a
2(1) screw along the shortest and longest cell edges as Eleanor says, which
would make the space group P 21 2 21 for the data set used in the Phaser run
with the data merged in P222. The merging statistics are equally good for all
3 2-folds and for the identity, which implies, as Eleanor says, that the data
most likely should be merged as orthorhombic. If the data were twinned that
would explain merging in higher symmetry even if the true space group were some
version of P2 or P21, but the twinning statistics look pretty close to what one
would expect for an untwinned crystal.
Maybe you’ve run Phaser in all 8 possible orthorhombic space groups in some
other job, but in the job that the file name implies was run in P212121, it was
actually only run in P222, i.e. the point group in which the data were merged.
So this job has missed all the more likely space groups.
What Phaser flags as an outlier rejection changed a couple of years ago, though
we still haven’t published this. For a long time, Phaser has rejected
improbably large structure factors, i.e. ones that would be expected to occur
less than one time in a million according to the Wilson distribution. For
about 2 years now, it has also been ignoring reflections flagged as containing
very little information about the true intensity, i.e. ones in which the
standard deviation of the intensity (SIGI) is large compared to the Wilson
expected intensity. When a crystal has very high anisotropy (as in this case,
where the anisotropic delta B, or the difference between the weakest and
strongest directions, is nearly 60 A^2, many of the reflections in the weak
directions in reciprocal space will contain so little information that they can
be ignored in the calculation (because they would contribute almost nothing
apart from raising the CPU time!). The presence of tNCS introduces more
reflections that are systematically very weak, as well. I should probably
change the log file output to separate the counts for the rejections vs the
ones being ignored. There are data sets where nearly half of the reflections
end up being ignored, so I wouldn’t worry about that for this data set.
Best wishes,
Randy Read
-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail:
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.
www-structmed.cimr.cam.ac.uk
> On 11 Aug 2018, at 20:36, Eleanor Dodson
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Marcelo - there is something very wrong with the data. You dont to reprocess
> in other space groups - the P2/mmm symmetry looks convincing but PHASER says
> there are 3500 rejections! That is an awful lot - 10 is a more normal value.
> I cant see the image clearly but something is causing problems. Split
> crystal? How are you processing it?
>
> The Moments go crazy at high resolution. Maybe try redoing the MR &
> refinement all at 3A?
>
>
> The MR rotation function solution is wonderful, but you need to conside
> spacegroups P 21 2 21. and P 21 21 21 .
> The translation vector of 0 0.5 0.13 would produce absences along the b axis.
> The screw axes along a and c look safe.
>
>
>
> On 11 August 2018 at 19:36, Marcelo Liberato
> wrote:
> I am sorry. I forgot to attach the image.
>
> Cheers
>
> Marcelo
>
> Em sáb, 11 de ago de 2018 às 18:31, Marcelo Liberato
> escreveu:
> Dear Eleanor,
>
> Thanks for you answer.
> Indeed, there are clear ice rings in the images (example attached). So, I
> integrated again (P1, P2 and P222) excluding the resolution ranges 2.28-2.22
> and 3.70-3.64. I am attaching the log files from aimless, MR and refmac for
> P2 (in two different cells) and P222 data.
> I agree that MR seems very good (in all cases), but the final density maps
> are always bad. Maybe the data has problems that I am not dealing with.
>
> Kind regards
>
> Marcelo
>
> Em sáb, 11 de ago de 2018 às 16:04, Eleanor Dodson
> escreveu:
> This MR looks good to me, but there are serious flaws with the data. Your
> secon moment plot from the aimless log has most spectacular spikes which are
> always a BAD THING, and the Wilson plot is not very smooth either..
>
> As Randy says, try to sort those problems out first.
>
> Then you have this message:
>
>
> TRANSLATIONAL NCS:
>
> Translational NCS has been detected at ( 0.000, 0.500, 0.125).
> A translation of 0.5 along B will generate pseudo-absences along b so you can
> be sure whether there is a scre axis or not..
>
> The space group is most likely orthorhombic - these indicators are pretty
> convincing for P2/mmm - so I dont know why you have chosen P21 as the
> spacegroup?
