Without making any calculations, the air scattering from the direct  
beam is an important contribution to the background. The image below  
is from a routine collection in our home source. I did force the gray  
scale a bit to make the point, but the "light shadow" to the lower  
right part of the image is actually the shadow of that air scattering  
by the crystal mounting pin (note how this "shadow" blocks part of  
the background as the beam-stop holder does, but does not block the  
diffracted spots).
In this particular image, the background counts in that area are  
about 15% less than out of it. Probably not enough to justify the  
hassle of a helium box, but enough sometimes to make the resolution  
limit in that area better than elsewhere.

Cheers,

Jose.

**************************************
Jose Antonio Cuesta-Seijo
Cancer Genomics and Proteomics
Ontario Cancer Institute, UHN
MaRS TMDT Room 4-902M
101 College Street
M5G 1L7 Toronto, ON, Canada
Phone:  (416)581-7544
Fax: (416)581-7562
email: [log in to unmask]
**************************************






On Nov 25, 2007, at 8:47 PM, Thomas Earnest wrote:

>> This is true, but if we really took the air-scatter argument  
>> seriously we
>> would go back to the days of huge Helium-filled enclosures to get  
>> rid of
>> the air scatter.  Some beamlines currently do direct He outflow  
>> from the
>> collimator toward the crystal, which reduces air scatter by the
>> indident beam, but I have not seen many beamline "helium box"  
>> setups to
>> reduce also the air scatter from the diffracted beams.
>>
>
>
> Reducing air scatter between the collimator and beamstop makes the  
> most significant reduction due to x-ray induced scattering background.
> Simply thinking, calculate the intensity times path-length before  
> the beamstop and compare to the scattered beam intensity times
> the diffracted path length to estimate. This would suggest air- 
> scatter from the diffracted beams (even totaled up) is small.
>
> Absorption/attenuation of the diffracted beam is an issue that can  
> be addressed by the He-box, and this air scatter should be balanced
> against window(s) on the He-box that also absorb. My impression is  
> that there are a few extreme cases where He box improves
> data quality, but that this is rarer than the number of cases where  
> it is used.....it would be nice to have someone perform
> a systematic study of this across a number of condition cases.
>
> IMHO mini-beams (at least those which retain a small divergence)  
> are critical for small crystals and rods where otherwise multiple
> crystals would be needed, and seem to make a significant difference  
> a number of cases, including mosiacity scanning as was
> earlier mentioned.
>
>
> - Thomas
>
> Thomas Earnest, Ph.D.
> Senior Scientist and Group Leader
> Structural Proteomics Development Group
> Physical Biosciences Division
> MS64R0121
> Lawrence Berkeley National Laboratory
> Berkeley CA 94720
>
> [log in to unmask]
> 510 486 4603
>
>
>
>
> Ethan A Merritt wrote:
>> On Sunday 25 November 2007 14:43, Ronald E Stenkamp wrote:
>>
>>
>>> Just a few comments on "consider a crystal bathed in a uniform  
>>> beam".
>>>
>>
>>
>>> Anyway, I thought the reason people went to smaller beams was that
>>> it made it possible to resolve the spots on the film or detector.  
>>> Isn't that the main reason for using small beams?
>>>
>>
>> If you mean that the projected image of the crystal onto the detector
>> is smaller because of a smaller beam, I think could only be  
>> relevant in
>> the case of truly huge crystals.  On the other hand, as mentioned  
>> earlier
>> in this thread, there is a possibility that a small beam will  
>> illuminate
>> a sweet spot on the crystal with lower mosaicity.  In that case yes,
>> the smaller beam may make it possible to resolve spots that would
>> otherwise overlap due to high mosaicity.
>>
>> I think that is the strongest argument being advanced recently for
>> the use of micro-beam apparatus.
>>
>> The other argument is that a smaller beam will generate lower  
>> background
>> due to air-scatter.  So for weakly diffracting crystals you want a  
>> beam
>> that is no bigger than the crystal, as any part of the beam that  
>> doesn't
>> hit the crystal contributes to the background but not to the signal.
>> This is true, but if we really took the air-scatter argument  
>> seriously we
>> would go back to the days of huge Helium-filled enclosures to get  
>> rid of
>> the air scatter.  Some beamlines currently do direct He outflow  
>> from the
>> collimator toward the crystal, which reduces air scatter by the
>> indident beam, but I have not seen many beamline "helium box"  
>> setups to
>> reduce also the air scatter from the diffracted beams.
>>
>>
>>> I'm less convinced that frame-to-frame scaling can correct for  
>>> absorption very well.  Due to our irregular-shaped protein crystals,
>>> before the area detectors came along, we'd use an empirical  
>>> correction
>>> (one due to North comes to mind) based on rotation about the phi  
>>> axis
>>> of a four-circle goniostat.
>>>
>>
>> The current scaling algorithms for area detectors do more than  
>> generate
>> a frame-to-frame scale. Separate correction factors are routinely
>> calculated for different regions of the diffraction image.
>> These map back onto a set of approximately equal X-ray paths through
>> the crystal. Furthermore, the 3D profile fitting done by some  
>> processing
>> programs is a logical extension of those same empirical  
>> corrections that
>> we did back in the 70s.
>>
>>
>>> It'd be interesting to determine the validity of the assumption that
>>> absorption is simply a function of frame number.
>>>
>>
>> I don't think any of the current generation of programs make that
>> assumption.  But maybe I'm giving them too much credit?
>>
>>