Hi,

I'm just catching up on the BB after the CCP4 Study Weekend!

Going back to the beginning of this thread, it's true that tNCS and twinning have opposite effects on the intensity moments, which can mask each other.  However, for simple cases (as this one appears to be) with a single NCS translation, the tNCS analysis in Phaser seems to be pretty successful at deconvoluting those effects.  It would be interesting to see the overall second moments and the second moments as a function of resolution from a run in Phaser, either in NCS mode or in MR_AUTO mode.

In such a case, once the tNCS is properly characterised, Phaser places molecules in pairs (or higher multiples in more complex cases of higher-order tNCS).  That should deal automatically with cases like the ones Phoebe mentions, where you could temporarily reduce the cell by a factor of two, but it works more generally when the tNCS doesn't correspond to a cell doubling.  We'd appreciate hearing about any cases where reindexing in a smaller cell works and Phaser's automated treatment didn't!  Or, indeed, about cases like the one Ethan mentioned where turning off the automatic tNCS correction helped.  (I've already been in touch with Ethan off-line.)

As Jacob and others have mentioned, you will always get lower R-factors once you treat the data as being twinned, and the more twin operators the bigger the reduction in R-factors.  So you need very strong evidence, independent of R-factors, to invoke twinning.  In this case, the L-test should be reasonably trustworthy even in the presence of tNCS, and your L-test values are close to what one would expect for an untwinned crystal.  At most you have partial twinning, or perhaps twinning of a pseudo-symmetric crystal (a possibility Phil mentioned), where the effects on intensity statistics are reduced.

One way to address a problem like this is to solve the structure in a lower symmetry space group (as you have done), but then to check whether the MR solution actually obeys the higher symmetry.  You can do this by looking at the crystal packing or at merging statistics for Fcalcs after a refinement with highly restrained NCS.  A similar sort of analysis is automated in the Zanuda tool in CCP4.

Dealing with potential complications from combinations of twinning and pseudosymmetry is one of the more challenging aspects of crystallography, but it's a good learning experience.  Good luck!

Randy Read

> On 10 Jan 2019, at 22:38, Donghyuk Shin <[log in to unmask]> wrote:
>
> Dear all,
>
> Thank you very much for all of your suggestions and sharing experiences.
> As many of you commented, the current small unit cell C2 refinement seems to be incorrect or correct, and I should put some efforts to crack this question.
>
> - To Phill Jeffrey,
> The idea, trying to find high symmetry SG with small unit cell C2 data is good idea, and I will try this.
> For your last comments, identifiable electron density differences between each chain,
> I guess there should not be other densities between chains if my current SG and model is correct. Am I right?
>
> - To Ethan,
> Turning off the automatic_tNCS_option seems to be good option.
> I think, my current data seems to be twinned then tNCS which I am not sure at this moment. But I will keep your advice in my mind.
>
> - To Phoebe A. Rice,
> It is quite interesting that you also could get structure solution by indexing strong spots and having smaller unit cell.
> Actually, I was wondering how it was possible that having half-sized unit cell could have solution, while full-sized unit cell could not.
> It will be great if you can share your experience a bit more (e.g the size of smaller unit cell used in initial search for both 1szp and 3pkz)
>
> Again, thank you very much for all of your suggestion.
>
> Best wishes,
> Donghyuk
>
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------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
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