[ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] [ccp4bb] translational NCS & twinning
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 (S
Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] [ccp4bb] translational NCS & twinning
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 fi
[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] [ccp4bb] translational NCS & twinning
Dear Philippe, As Randy just pointed out, when twinning, pseudosymmetry and other pathologies come into play, things really get complicated. I agree with what you said but for the current problem, things may be more complicated. To summarize: - "bona fide" twinning: there are two different, intergrown crystals and the intensities of both crystals just add up. - "nano scale" twinning, called statistical disorder: the two orientations are randomly distributed through the crystals and the diffraction of both conformations interferes. The conformations behave like alternate conformations. - Twinning/pseudosymmetry/wrong unit cell etc.: Here the two conformations, present in the large (true) unit cell and related by crystallographic or noncrystallographic symmetry, may not fit in the small (false) unit cell and be accounted for by introducing twinning where none is present. Especially with 6 twinning operators, the refinement programs have a lot of room to tweak around to reduce the R-factors. Therefore my advice would be: - Critically check the space group and especially how weak are the weak reflections discarded with the small unit cell? - the solution you got in the small unit cell may be a subset of what is present in the large unit cell, so I would also try molecular replacement with the ensemble of molecules you got in the small unit cell. My two cents, Herman -Ursprüngliche Nachricht- Von: DUMAS Philippe (IGBMC) [mailto:p.du...@ibmc-cnrs.unistra.fr] Gesendet: Freitag, 11. Januar 2019 11:52 An: Schreuder, Herman /DE Cc: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] [ccp4bb] translational NCS & twinning 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
[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] [ccp4bb] translational NCS & twinning
Le Vendredi 11 Janvier 2019 12:18 CET, a écrit: Thank you Herman you for this clear and informative comments !! Particularly your last point, which I found very instructive. Now I remember the title of the article by T.O. Yeates "Protein crystals and their evil twins" in 1999. And this corresponds well to the difficulty of the problem. Philippe D. Philippe Dumas > Dear Philippe, > > As Randy just pointed out, when twinning, pseudosymmetry and other > pathologies come into play, things really get complicated. > I agree with what you said but for the current problem, things may be more > complicated. > > To summarize: > - "bona fide" twinning: there are two different, intergrown crystals and the > intensities of both crystals just add up. > - "nano scale" twinning, called statistical disorder: the two orientations > are randomly distributed through the crystals and the diffraction of both > conformations interferes. The conformations behave like alternate > conformations. > - Twinning/pseudosymmetry/wrong unit cell etc.: Here the two conformations, > present in the large (true) unit cell and related by crystallographic or > noncrystallographic symmetry, may not fit in the small (false) unit cell and > be accounted for by introducing twinning where none is present. Especially > with 6 twinning operators, the refinement programs have a lot of room to > tweak around to reduce the R-factors. > > Therefore my advice would be: > - Critically check the space group and especially how weak are the weak > reflections discarded with the small unit cell? > - the solution you got in the small unit cell may be a subset of what is > present in the large unit cell, so I would also try molecular replacement > with the ensemble of molecules you got in the small unit cell. > > My two cents, > Herman > > > -Ursprüngliche Nachricht- > Von: DUMAS Philippe (IGBMC) [mailto:p.du...@ibmc-cnrs.unistra.fr] > Gesendet: Freitag, 11. Januar 2019 11:52 > An: Schreuder, Herman /DE > Cc: CCP4BB@JISCMAIL.AC.UK > Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] [ccp4bb] translational NCS > & twinning > > > 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 > > Betr
