Simple algorithm for a maximum-likelihood SAD function.

By A. McCoy, L. C. Storoni, Randy J. Read. 2004

106 citations recorded by the source corpus.

Recently, the multivariate complex normal distribution has been used to develop a maximum-likelihood probability function for single-wavelength anomalous diffraction phasing and refinement of heavy-atom parameters [Pannu & Read (2004), Acta Cryst. D60, 22-27]. The function accounts explicitly for the correlations between the observed and calculated Friedel mates and their errors. However, the method of derivation of the equation described by Pannu & Read (2004) leads to a complicated likelihood expression that suffers from a number of algorithmic limitations. Here, an alternative derivation of the P(SAD) function is described that leads to simplified algorithmic requirements and that allows an intuitive understanding of the expression.

Subfields: Food Science

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Citations in the corpus

• Using SAD data in Phaser (2011, neutral): “The SAD likelihood function (McCoy et al., 2004) is the joint distribution of the amplitudes for the plus and minus hands given the contributions computed from the anomalous scatterer model.”
• Phaser crystallographic software (2007, background): “The SAD likelihood function explicitly accounts for the correlations between FþO and F O (McCoy et al., 2004; Pannu & Read, 2004).”
• Recent developments in phasing and structure refinement for macromolecular crystallography (2009, background): “However, the case of single-wavelength anomalous diffraction (SAD) can be handled without such assumptions [12].”
• Serial femtosecond crystallography: the first five years (2015, methodology): “However, SAD approaches rely on a good error model of the measured amplitudes (McCoy, 2004; McCoy et al., 2004).”
• Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing (2016, methodology): “The substructure and the anomalous differences are then used together to estimate crystallographic phases for the entire structure (Hendrickson & Teeter, 1981; Wang, 1985; Otwinowski, 1991; de La Fortelle & Bricogne, 1997; Furey & Swaminathan, 1997; McCoy et al., 2004; Pannu & Read, 2004).”
• Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal (2016, methodology): “For each data set, phase calculations were carried out with Phaser (McCoy et al., 2004) using the known anomalous substructure and the measured anomalous differences for the data set.”