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 > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ ----- 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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
