Le Vendredi 11 Janvier 2019 09:07 CET, herman.schreu...@sanofi.com a écrit:
Dear Herman, As far as I understood the twinning problem, what you say is only true in some occasions, and not in others. If the "macroscopic" domains are so small that they are smaller than the X-rays coherence length, then you may do what you say because the X-rays emitted by the different domains can interfere. But, if the domains become large, the X-rays emitted by the different domains do not interfere anymore and you have to add the weighted intensities, not the amplitudes, of each domain. I hope I understood well your comment and did not "interfere negatively" with the thread... Best Philippe Dumas > Dear Lan, > > Thank you for your compliment. I do not use Xtriage, so I did not bother > looking at the log files. > > What I meant to say is that with twinning, the crystal has different > macroscopic domains where the molecules have different orientations, say one > domain with orientation A and one domain with orientation B. Since these > domains grow on top of each other, they are usually related by a twin > operator similar to a crystallographic operator such as a twofold axis. > The fourier transform of the electron density of the crystal is the > convolution of the fourier transform of the individual molecules with the > crystal lattice, with the fourier transform of the individual molecules > usually giving the stronger contribution. So to get a solution with a decent > R-factor, one must include all orientations (A, B etc.) in the model, with > the position of the molecules in the crystal lattice contributing less to the > diffraction pattern. So one can put the orientations on top of each other in > a small unit cell using twinning, or put them in a larger unit cell at > different positions using crystallographic or non-crystallographic symmetry. > That is what I meant be "twinning" (N)CS. > > Hope this makes my remark a little clearer. > > Best, > Herman > > PS: While other BB readers may have had the same question, I have posted the > reply to the BB. I hope you don't mind. > > > -----Ursprüngliche Nachricht----- > Von: Guan, Lan [mailto:lan.g...@ttuhsc.edu] > Gesendet: Donnerstag, 10. Januar 2019 20:53 > An: Schreuder, Herman /DE > Betreff: Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] translational NCS & twinning > > Dear Herman, > I have read your insightful comments on twining and tNCS for years now, which > is very useful and helpful! Thanks, > > For Donghyuk’s case, do you think that he really has a twinning issue? With > a lower symmetry, all possible twining operators is always reported in the > Xtriage and did not mean a real twin existed. His L test shows a twin > fraction of 0.00 in his log file. The intensity statistics does not really > indicate an actually twinning. Base on the refinement, twin law is needed to > get refinement going. It looks like a twin. I am confused... > > > the molecules are related by "twinning" (N)CS? > > > What does this mean “ twinning (N)CS"? Would you please kindly explain it > further? > > Thanks, > > > Lan > > > ******************************************************************************************** > Lan Guan, MD PhD > Associate Professor | Department of Cell Physiology and Molecular Biophysics > Director | Center for Membrane Protein Research > > 3601 4th St. MS 6551 | Lubbock, TX 79430 > 5A148A (Office) | (1) 806 743-3102 (Phone) | lan.g...@ttuhsc.edu (E-Mail) > > http://www.ttuhsc.edu/medicine/cell-physiology-molecular-biophysics/faculty/guan/ > https://www.ttuhsc.edu/centers-institutes/membrane-protein-research/ > ******************************************************************************************** > > > On Jan 10, 2019, at 11:10 AM, herman.schreu...@sanofi.com wrote: > > > > CAUTION: This email originated from outside of TTUHSC. Do not click links > > or open attachments unless you recognize the sender and know the content is > > safe. > > > > > > Dear Donghyuk, > > > > Unfortunately, everything is possible when NCS, twinning etc. get into the > > game. I do not have answers, but some questions for you to think about: > > - Do you really have 6 twinning operators, or only one operator and are the > > other operators generated by (non)crystallographic symmetry? > > - Both your P6322 cell and your C2 cell have angles of 90 90 90. For P6322, > > the last angle should be 120 and for C2, only the second angle is > > constrained to be 90. Maybe you should check that not somewhere something > > went wrong with the cell angles. > > - How weak are the reflections that got discarded by halving the a- and > > b-axes? Do they have significant intensity, or is it only noise? > > - By shrinking the unit cell, you may have created artificial twinning when > > in the large unit cell the molecules are related by "twinning" (N)CS. > > - Since you seem to have found a solution with the small unit cell, you > > could see if you could fit this solution in the large unit cell: Process in > > P1 in the large unit cell and use the ensemble (the complete! unit cell of > > your C2 solution, as a search model. > > - Your current solution maybe correct after all, but I would analyze it > > very critically. > > > > Best, > > Herman > > > > > > -----Ursprüngliche Nachricht----- > > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von > > Donghyuk Shin > > Gesendet: Donnerstag, 10. Januar 2019 11:12 > > An: CCP4BB@JISCMAIL.AC.UK > > Betreff: [EXTERNAL] [ccp4bb] translational NCS & twinning > > > > Dear all, > > > > I am having tough time with my Xtal data sets those seem to be twinned or > > have translational NCS, and it will be greatly appreciated if you can give > > me some advices or comments! > > > > Data was initially processed with XDS and scaled with aimless without > > specifying certain space group (SG). > > Aimless picked the P 63 2 2 for the best SG, but the xtriage indicates > > there is non-origin peak after patterson analysis. (attached log) And, I > > could not get the proper MR-solution from this data sets. > > > > Because I read that twinning and tNCS cannot be properly distinguished at > > high SG, I went down to subgroup either P32 or P6 assuming that there is > > twinning which make data set seems to have apparently high SG. (procedure > > was same XDS->aimless but I specified the SG to keep them) Then, xtriage > > still indicates there is non-origin peak as before, but found twin laws for > > the data sets (attached log). > > However, I still could not get the right MR-solution. > > Then, I went even further down to P3 or C2, and xtriage found more twin > > laws which is make sense because of the lower SG. (attached log) Again, I > > could not get the MR-solution. > > For all the MR running above, I assumed that phaser(ccp4 module) > > automatically applied tNCS if they present. or should I have to tick on > > button in the expert parameters? > > > > Then, I went back to the image and processed the datasets with mosflm by > > checking the indexed spots. > > During this step, I played with the threshold for indexing to follow the > > strong spot for get correct SG. > > I am not sure whether this is correct or not, but by putting high threshold > > for indexing (e.g. ~15) I could index the data with C2 which has half > > dimension for a,b axes (116.348, 67.218, 182.861, 90, 90, 90) to the > > original unit cell (232.533, 134.202, 182.67, 90, 90, 90). > > With this, I could put 3 molecules in ASU by MR. During refinement, I felt > > that the R values were not dropping, and I applied twin refinement. > > without twin refinement the R values were (0.39/0.44, work/free), and > > applying twin refinement gave me significantly better values (0.23/0.26). > > Because there were 6 twin operators which may cause this huge R value drop, > > I speculate whether this is true or not. > > > > Your comments will be greatly helpful! > > > > With you all the best, > > 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=DwIFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=xlZKtKm2eNS0qmQb4wXnIIknGL1-n0M0toJoWb2Ezco&s=scEheHieLBLhJMaXoEDimlYM9TAk600XwBjYXrQC1nc&e= > > > > ######################################################################## > > > > 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=DwIGaQ&c=dIAUvHjI5lMnDD45iB3vgA&r=SZfWxbou0cinb5MH936uQKMweCFFe1qb2Aj8yA2JJ_E&m=CXwJp-j1r20_EFFgLa_63BLe7UOJ_fKi7GSbbYQVSZs&s=ZR_6New6L1BTQUi3oiOpez9wEkwELOw00gGuGtu7L7E&e= > > > ######################################################################## > > 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
