Dear Lan, Yes, that’s a serious problem that has led some people astray, including a few papers where people got apparently good R-factors by invoking non-existent twinning.
You can find a brief discussion of this point on the CCP4 wiki (https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/R-factors), which has links to a couple of publications where Garib Murshudov has worked out what happens to R-factors when you treat the data as twinned even when it isn’t. Best wishes, Randy ----- 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: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > On 11 Jan 2019, at 23:05, Guan, Lan <lan.g...@ttuhsc.edu> wrote: > > Hi Randy, > > >> 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. > > Do normal data with no twinning, but refined with twin operator(s), show > similar phenomenon? If it decreases R-factors for normal data, how much it > can achieve (5-10% lower)? > > Thanks, > > > Lan > > > >> 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 <sdh...@gmail.com> 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://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFAg&c=dIAUvHjI5lMnDD45iB3vgA&r=SZfWxbou0cinb5MH936uQKMweCFFe1qb2Aj8yA2JJ_E&m=1tRkoB-BHhBWDCtbPikRHJfYIDIqpaGbVoF5xFjTLD4&s=007v9D7bqs0h2uVFwau-m4cmT4PVlWyYZ2UVxJvWkrs&e= >> >> ------ >> 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: 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://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFAg&c=dIAUvHjI5lMnDD45iB3vgA&r=SZfWxbou0cinb5MH936uQKMweCFFe1qb2Aj8yA2JJ_E&m=1tRkoB-BHhBWDCtbPikRHJfYIDIqpaGbVoF5xFjTLD4&s=007v9D7bqs0h2uVFwau-m4cmT4PVlWyYZ2UVxJvWkrs&e= > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
