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 <[email protected]> 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 <[email protected]>
>> 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
>
