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Hi Jacob,

both George Sheldrick and Andrew Leslie explained to me that the
machine I had in mind - a sealed tube generator with a graphite
monochromator - is not really state of the art and merely a technology
from 20 years ago. Hence my comment about the top hat profile of
inhouse machines adding to the high quality data they produce was
inappropriate. Modern inhouse machines usually don't show a top hat
profile.

The quote from Bruker I referred to addressed a project to check
crystals before collecting neutron data, where such a machine is
indeed appropriate. However, most of us hardly ever see crystals with
a volume in the mm^3 region.

Sorry if I caused any confusion - I felt I should set this straight
for everyone to know.

Cheers,
Tim

On 01/12/2015 11:32 PM, Keller, Jacob wrote:
>> 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.
> 
> I assume that the synchrotron data were collected at similarly-low
> energy?
> 
>> 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.
> 
> Yes, I haven't seen much about people collecting multiple
> orientations of the same crystal, since I think people generally
> roast their crystals really fast to see higher-resolution spots. I
> am thinking recently that the best option might really be home
> sources with pixel-array detectors...
> 
>> 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.
> 
> Pretty interesting--wonder what's the best way to confirm this for
> our home source...?
> 
> JPK
> 
> 
> 
> 
> 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
>> <[log in to unmask]> 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
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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