Ab initio low-resolution phasing in crystallography of macromolecules by maximization of likelihood.
Statistical likelihood criteria were tested to select the true (or closest to true) structure-factor phases from an ensemble of phase sets. To define the criterion value for a given trial phase set, the trial 'molecular region' is defined as a region consisting of the points with the highest values in the Fourier synthesis calculated with the observed magnitudes and the trial set of phases. The structure studied is considered as composed of atoms randomly placed inside the trial molecular region. The figure of merit is defined as the likelihood corresponding to this hypothesis, i.e. the probability that the structure-factor magnitudes calculated (from the positions of atoms randomly placed into the trial region) are equal to the observed magnitudes. The concept of generalized likelihood is introduced to make the calculations more straightforward. The tests performed for known structures with the use of experimentally observed magnitudes show that in general it is impossible to unambiguously determine the best phases among a 'population' of trial phase sets. Nevertheless, the random generation of a great number of phase sets and the selection of phase sets with high likelihood values give a collection of variants with a higher concentration of 'good' phase sets than those found in the original population. Averaging the selected phase sets gives a starting solution of the low-resolution phase problem.
Petrova
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TE
Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142292, Russia.
Lunin
V Y
VY
Podjarny
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AD
D003459:Crystallins / Q000737:chemistry*; D016013:Likelihood Functions; D008962:Models, Theoretical; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D012349:RNA, Transfer, Asp / Q000737:chemistry*; D014961:X-Ray Diffraction / Q000379:methods*
D003459:Crystallins; D012349:RNA, Transfer, Asp