-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Jacob,
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 On 01/08/2015 06:47 PM, Keller, Jacob wrote: > Yes, this is great info and thoughts. What I still do not > understand, however, is why the noise from air/loop scattering is > so bad--why not make sure only the top of the Gaussian is engulfing > the crystal, and the tails can hit air or loop? Isn't the air > scattering noise easily subtractable, being essentially flat over > time, whereas uneven illumination of the crystal is highly > difficult to correct? > > Also, in light of these considerations, it would seem to me a much > better use of resources not to make brighter and smaller beams but > instead concentrate on making better low-intensity big beam > profiles (top-hats?) and lower-noise, faster detectors (like > Pilatus and the new ADSC). > > Jacob > > -----Original Message----- From: James Holton > [mailto:jmhol...@lbl.gov] Sent: Tuesday, December 30, 2014 3:57 PM > To: Keller, Jacob; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How > far does rad dam travel? > > > Yes, bigger is okay, and perhaps a little better if you consider > the effects of beam/crystal vibration and two sharp-edged > boundaries dancing over each other. But bigger is better only to a > point. That point is when the illuminated area of non-good-stuff > is about equal to the area of the good stuff. This is because the > total background noise is equal to the square root of the number of > photons and equal volumes of any given "stuff" (good or non-good) > yield about the same number of background-scattered photons. So, > since you're taking the square root, completely eliminating the > non-good-stuff only buys you a gain of 40% in total noise. Given > that other sources of noise come into play when the beam and > crystal are exactly matched (flicker), 40% is a reasonable > compromise. This is why I recommend loop sizes that are about 40% > bigger than the crystal itself. Much less risk of surface-tension > injury, and the air around the loop scatters 1000x less than the > non-crystal stuff in the loop: effectively defining the "beam > size". > > As for what beam profiles look like at different beamlines, there > are some sobering mug-shots in this paper: > http://dx.doi.org/10.1107/S0909049511008235 > > Some interesting quirks in a few of them, but in general optimally > focused beams are Gaussian. Almost by definition! (central limit > theorem and all that). It is when you "de-focus" that things get > really embarrassing. X-ray mirrors all have a "fingerprint" in the > de-focused region that leads to striations and other distortions. > The technology is improving, but good solutions for "de focusing" > are still not widely available. Perhaps because they are hard to > fund. > > Genuine top-hat beams are rare, but there are a few of them. > Petra-III is particularly proud of theirs. But top-hats are > usually defined by collimation of a Gaussian and the more x-rays > you have hitting the back of the aperture the more difficult it is > to control the background generated by the collimator. If you can > see the shadow of your pin on the detector, then you know there is > a significant amount of "background" that is coming from upstream > of your crystal! My solution is to collimate at roughly the FWHM. > This chops off the tails and gives you a tolerably "flat" beam in > the middle. > > How much more intense is the peak than the tails? Well, at the > FWHM, the intensity is, well, half of that at the center. At twice > that distance from the center, you are down to 6.2%. The equation > is exp(-log(16)*(x/hwhm)**2) where "hwhm" is 1/2 of the FHWM. > > HTH! > > -James Holton MAD Scientist > > On 12/30/2014 12:10 PM, Keller, Jacob wrote: >>> Yes, it gets complicated, doesn't it? This is why I generally >>> recommend >> trying to use a beam that matches your crystal size. >> >> ...or is bigger, right? Diffuse scattering, yes, but more even >> illumination might be worth it? >> >> Generally, James, I have a question: what is the nature of the >> intensity cross-sections at most beamlines--are they usually >> Gaussian, or are some flatter? Or I guess, if Gaussian, how much >> more intense is the peak than the tails? >> >> JPK >> >> > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) iD8DBQFUr5VDUxlJ7aRr7hoRAmheAKCaaSSzZYBr5qZicBhkhmAljJQA4ACdFSgk LX6wrM7dUvK55C2TI/cIDj0= =lt/w -----END PGP SIGNATURE-----
