Hi Tim, Jacob, I must admit that I was very surprised by the suggestion of a top-hat profile for a in-house rotating anode. We have a Rigaku Fr-E generator, and Rigaku provided a plot of the beam profile for that (with VariMax-HR Optic) and it is very far from being top hat, much more Gaussian-like, which really is what I would have expected for this type of source and optic.
Without significantly truncating the full profile (i.e. by selecting the very central part of a Gaussian, which results in a significant loss of flux) I don't know how they would achieve a top hat profile, but perhaps someone from Bruker could respond to this ? I guess my point is that certainly not all in house generators provide a beam with a top hat profile. Best wishes, Andrew On 12 Jan 2015, at 21:38, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote: > Hi Jacob, > > at the beginning of my experience of S-SAD about 10 years ago, it was > not too difficult to do S-SAD phasing with inhouse data provided the > resolution was better than 2.0A, while it did not always work with > synchrotron data. Purely personal experience. > > However, the inhouse machines I am familiar with have three circles, so > that you get much better real redundancy with equivalent reflections > recorded at different settings. This reduces systematic errors, I think. > The most sophisticated synchrotron beamline I have been to offered a > mini-kappa with 30degree range - that's not much compared to 10-20 > different settings with varying phi- omega- and distance settings. > > The top-hat comes from a quote I received from Bruker, and I have no > reason to believe the person acted purely with a salesperson's intent. > > Best, > Tim > > On 01/12/2015 09:05 PM, Keller, Jacob wrote: >>> the top-hat profile is one of the reasons why inhouse machines produce >>> better quality data than synchrotrons. However, the often much increased >>> resolution you achieve at the synchrotron is generally worth more than the >>> quality of the data at restricted resolution. >>> >>> Cheers, >>> Tim >> >> Several surprises to me: >> >> -Data from in-house sources is better? >> I have not heard of this--is there any systematic examination of this? >> I saw nothing about this in a very brief Google foray. >> >> -In-house beam profiles are top-hats? >> Is there a place which shows such measurements? Does not pop out of >> Google for me, but I would love to be shown that this is true. >> >> -Resolution at the synchrotron is better? >> This does not really seem right to me theoretically, although in >> practice it does seem to happen. I think it is just a question of waiting >> for enough exposure time, as the CCP4BB response quoted at bottom describes. >> >> JPK >> >> >> >> =========================== >> >> >> Date: Tue, 12 Oct 2010 09:04:05 -0700 >> From: James Holton <jmhol...@lbl.gov> >> Re: Re: Lousy diffraction at home but fantastic at the synchrotron? >> There are a few things that synchrotron beamlines generally do better than >> "home sources", but the most important are flux, collimation and absorption. >> Flux is in photons/s and simply scales down the amount of time it takes to >> get a given amount of photons onto the crystal. Contrary to popular belief, >> there is nothing "magical" about having more photons/s: it does not somehow >> make your protein molecules "behave" and line up in a more ordered way. >> However, it does allow you to do the equivalent of a 24-hour exposure in a >> few seconds (depending on which beamline and which home source you are >> comparing), so it can be hard to get your brain around the comparison. >> Collimation, in a nutshell, is putting all the incident photons through the >> crystal, preferably in a straight line. Illuminating anything that isn't the >> crystal generates background, and background buries weak diffraction spots >> (also known as high-resolution spots). Now, when I say "crystal" I mean the >> thing you want to shoot, so this includes the "best part" of a bent, cracked >> or otherwise inhomogeneous "crystal". The amount of background goes as the >> square of the beam size, so a 0.5 mm beam can produce up to 25 times more >> background than a 0.1 mm beam (for a fixed spot intensity). >> Also, if the beam has high "divergence" (the range of incidence angles onto >> the crystal), then the spots on the detector will be more spread out than if >> the beam had low divergence, and the more spread-out the spots are the >> easier it is for them to fade into the background. Now, even at home >> sources, one can cut down the beam to have very low divergence and a very >> small size at the sample position, but this comes at the expense of flux. >> Another tenant of "collimation" (in my book) is the DEPTH of non-crystal >> stuff in the primary x-ray beam that can be "seen" by the detector. This >> includes the air space between the "collimator" and the beam stop. One >> millimeter of air generates about as much background as 1 micron of crystal, >> water, or plastic. Some home sources have ridiculously large air paths (like >> putting the backstop on the detector surface), and that can give you a lot >> of background. As a rule of thumb, you want you air path in mm to be less >> than or equal to your crystal size in microns. In this situation, the >> crystal itself is generating at least as much background as the air, and so >> further reducing the air path has diminishing returns. For example, going >> from 100 mm air and 100 um crystal to completely eliminating air will only >> get you about a 40% reduction in background noise (it goes as the square >> root). >> Now, this rule of thumb also goes for the "support" material around your >> crystal: one micron of cryoprotectant generates about as much background as >> one micron of crystal. So, if you have a 10 micron crystal mounted in a 1 mm >> thick drop, and manage to hit the crystal with a 10 micron beam, you still >> have 100 times more background coming from the drop than you do from the >> crystal. This is why in-situ diffraction is so difficult: it is hard to come >> by a crystal tray that is the same thickness as the crystals. >> Absorption differences between home and beamline are generally because >> beamlines operate at around 1 A, where a 200 um thick crystal or a 200 mm >> air path absorbs only about 4% of the x-rays, and home sources generally >> operate at CuKa, where the same amount of crystal or air absorbs ~20%. The >> "absorption correction" due to different paths taken through the sample must >> always be less than the total absorption, so you can imagine the relative >> difficulty of trying to measure a ~3% anomalous difference. >> Lower absorption also accentuates the benefits of putting the detector >> further away. By the way, there IS a good reason why we spend so much money >> on large-area detectors. Background falls off with the square of distance, >> but the spots don't (assuming good collimation!). >> However, the most common cause of drastically different results at >> synchrotron vs at home is that people make the mistake of thinking that all >> their crystals are the same, and that they prepared them in the "same" way. >> This is seldom the case! Probably the largest source of variability is the >> cooling rate, which depends on the "head space" of cold N2 above the liquid >> nitrogen you are plunge-cooling in (Warkentin et al. 2006). >> -James Holton >> MAD Scientist >> > > -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A >