Does the diffraction pattern change if you shoot the crystal from phi = n or n+180 deg (a la inverse-beam geometry)? I was thinking it was identical, but I am not sure now--is it a mirror image? Maybe different space groups are different?
JPK On Fri, Feb 11, 2011 at 10:35 AM, James Holton <[email protected]> wrote: > > The indexing ambiguities do not include anomalous pair confusion because > there is no way to rotate the lattice to make every h,k,l overlap with > -h,-k,-l. I.E. you can't rotate your left hand to superimpose it on your > right. The only way to mix those up is to change the sign of some detector > geometry parameter (I.E. looking in a mirror). > > That said, anomalous differences tend to be very weak and noisy in all but > the most exotic cases of macromolecular diffraction. Twinning makes this > worse because you are (to a first order approximation) averaging DANO(h,k,l) > with DANO(k,h,-l) and the result will tend to be closer to zero than either > one taken individually. However, the biggest source of error in LCLS > datasets at the moment is partiality. Basically, you only get one shot per > crystal, you can't rotate it appreciably in the 70 fs exposure time, the > beam is a laser so there is essentially no divergence or dispersion, and the > crystals are so small as to be one mosaic domain each, so there is no > "mosaic spread". The "3D profile" of the spots is therefore dominated by > the finite size of the crystal itself (Sherrer broadening). We were > actually worried for a while that we wouldn't see any spots at all at LCLS! > > So, everything is a partial, and we currently don't have postrefinement > software that can model the shape of each crystal and give us a partiality. > At least, not in a reasonable amount of time. If we spent 30 s on each of > the 3 million images, we would still be processing them for a few more > years. So, for the first run, it was decided to jut average out the > partiality errors. For example, unknown partiality means that each spot is > measured with 100% error (at best), but if you have 700 of them, then the > expected error of the average is ~3%. John Spence called this a "Monte > Carlo integration", and it turned out to be a really good idea. We measured > the error of the average by splitting the images into two heaps and > comparing the merged datasets that resulted from each heap. I proposed > calling this "R-internal" for internal agreement, since a traditional Rmerge > does not really apply. However, I admit that for the PDB deposition I > entered R-internal as "Rmerge". Technically, R-internal is exactly what an > Rmerge used to be: the R-factor between data from different crystals. > > Personally, I think "the way" to crack this "twin problem" is to scale all > the data and look at the partial intensity histograms for each spot. In > situations where the "true" values of h,k,l and k,h,-l have radically > different intensities, there will be a bimodal distribution, and that will > allow us to re-index the ~700 images that contained a spot from one of those > two hkls. Which group to flip (the bright ones or the dim ones) is an > interesting question, but probably the dim ones, since they are the least > consistent with the average intensity. Might need to try both. After > re-mergeing and re-scaling, there will be another hkl with the strongest > bimodal distribution, and then you iterate. That's the idea anyway. > > -James Holton > MAD Scientist > > On 2/10/2011 6:32 AM, Jacob Keller wrote: >> >> Would it be true that the anomalous differences could not be measured >> in these types of datasets, because one would not know which >> Friedel/Bivoet reflection one is measuring in a given frame? Perhaps, >> given anomalous signal, there would be a way to tease out which >> orientation one was looking at from the correlations of the >> signs/magnitudes of anomalous-scattering-induced deviations from the >> mean intensities (derived from the whole dataset) for all of the >> relections observed in each frame? I guess this might also detwin the >> data? >> >> JPK >> >> On Thu, Feb 10, 2011 at 7:17 AM, Anastassis Perrakis<[email protected]> >> wrote: >>>> >>>> Anyway, I thought that was a cool idea, but like so many other cool >>>> things, it had to be cut from the Nature paper. Admittedly, the problem >>>> has >>>> not actually been solved yet. This is why we used REFMAC in TWIN mode. >>> >>> Is that a hint on the: >>> >>> a. wisdom of the editor >>> b. wisdom of 'the third referee' >>> c. wisdom of the dogma 'five years of eight eight lifes in 2000 words' >>> d. All of the above >>> >>> ;-) >>> >>> A. >>> >> >> > > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: [email protected] *******************************************
