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[ccp4bb] questions on SF likelihood |
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CCP4bb navigationCCP4bb <-- 2007 <-- February 2007 <-- 28 February 2007Subject: questions on SF likelihood From: pam52 {- at -} CORNELL {- dot -} EDU Date: 2007-02-28 I've managed to do a pretty good job of confusing myself in my latest attempt to understand the likelihood stuff, and was hoping that I could get some pointers as to what I'm misunderstanding. 1. How does one determine the amplitude and phase to use from a given likelihood surface? Some of the papers I've read refer to using the centroid; others seem to be talking about using the location of the maxima. Is there any guidance for when you'd use one instead of the other, or is this one of those "try both and see which works best" situations? 2. How do you get the HL coefficients out of a likelihood surface? The only way I could think of to do this would be to pick up the likelihood values over the full phaser circle for a constant amplitude, and fit a 2-term fourier series to the ln of those values. But this approach feels more like a work-around than anything else (and would lead to the same point in complex space having two difference likelihoods for a centric reflection), so I'm fairly sure there's a better way to do this (although I don't have any ideas what that would be). SigmaA weights might be a possibility, but as far as I know they wouldn't work for all cases (MAD and SAS don't have native amplitude measurements). Thanks in advance for any help, Pete Pete Meyer Fu Lab BMCB grad student Cornell University CCP4bb navigationCCP4bb <-- 2007 <-- February 2007 <-- 28 February 2007 |
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