In the recent crystallography workshop in Thailand, we had at least 3 cases 
brought by participants where we had reason to suspect that the data had been 
over-merged because of undetected twinning. Often there is more than one 
possible twinning operator and (as potentially in one of the cases brought up 
recently on this BB) the easiest way to sort out the true symmetry is just to 
expand the data to P1 and solve the structure by looking for the appropriate 
expanded number of copies. If the data are of reasonable quality 
(case-dependent) and the model is good (true more often than not, in these 
post-AlphaFold days), the multicopy MR solution can be pretty straightforward. 
Once you have a better idea of the true symmetry, then would be a good time to 
try reprocessing the data without assuming too high symmetry. Why would we want 
to impose an arbitrary restriction on users for this relatively common scenario.

Note that this kind of confusion between twinning and true symmetry will mostly 
arise when the twin fractions are close to equal. Then: a) the twin-related 
intensities should really be measurements of the same thing, and you get more 
precise data by making them equal; b) the superimposed diffraction patterns 
will obey the higher symmetry, although the spots might start to split at 
higher resolution.

I would also argue that, if the twin fractions are experimentally 
indistinguishable from being equal, processing in higher symmetry and expanding 
the data to the correct lower symmetry is the correct approach to take for your 
final data set. Obviously you still want to try to process the data in the 
correct space group to make this decision, looking at things like whether the 
observations related by true symmetry are more highly correlated than 
observations related by the twin operator(s).

Best wishes,

Randy

> On 23 Feb 2024, at 10:39, Huw Jenkins 
> <0000288da93ae744-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> On 23 Feb 2024, at 09:58, Winter, Graeme (DLSLtd,RAL,LSCI) 
>> <00006a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> so strictly it is possible and correct - if experimentally unlikely - to 
>> have the situation we are discussing here occur.
>
> I believe this is only technically possible because the MTZ format does not 
> store esds on the unit cell parameters? In the thaumatin example processing 
> the dataset here  - https://zenodo.org/records/4916649 - assuming monoclinic 
> symmetry results in unit cell:
>
> 58.176(2), 150.543(4), 58.2050(18), 90.0, 90.1058(9), 90.0
>
> The situation you describe would result in for example:
>
> 58.1087(18), 150.543(4), 58.1087(15), 90.0, 90.0000(1), 90.0
>
> and the test should really only fail for:
>
> 58.1087(18), 58.1087(18), 150.400(5), 90.0, 90.0, 90.0
>
> i.e. where a=b have same value and esd (as they were constrained to be 
> identical and esd on beta is 0 as it was constrained to be 90.
>
>
>
>> Telling users to “fiddle the parameters” so that the strict test is 
>> satisfied feels like a non-ideal answer: a warning when importing such data 
>> could be legitimate e.g. “hmm I note a = b and al=be=ga=90 _exactly_ this is 
>> unusual, I hope you know what you are doing” rather than a flat out error
>
> I think you have misunderstood here. I was suggesting telling users to 
> integrate/scale the data without imposing higher symmetry was the correct 
> thing to do? I don't see how "fiddling of parameters" is required.
>
> But I agree i2 should allow an override of this test.
>
>
> Huw
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-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research     Tel: +44 1223 336500
The Keith Peters Building
Hills Road                                                       E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.                              
www-structmed.cimr.cam.ac.uk


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