 |
 |
That P6322 Xtriage shows pretty clearly that you have good data, and that it is not twinned.. So I think you stick with that spacegroup - introducing false twin laws to explain true crystal symmetry reduces the R values at the expense of getting clear electron density. You could process the data in a cell with the a b axes halved, choosing only the strong reflections not affected by the non-cryst Patterson vector, but in fact the MR programs take such a translation into account during structure solution . Eleanor Dodson On Fri, 11 Jan 2019 at 10:54, Randy Read <[log in to unmask]> wrote: > 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 > > > > ######################################################################## > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ------ > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: + 44 1223 336500 > Wellcome Trust/MRC Building Fax: + 44 1223 336827 > Hills Road E-mail: [log in to unmask] > 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/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1