A procedure compatible with X-PLOR for the calculation of electron-density maps weighted using an R-free-likelihood approach

By Alexandre Urzhumtsev, T. P. Skovoroda, Vladimir Y. Lunin. 1996

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Citations in the corpus

Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “Since the atomic parameters and the bulk-solvent model are updated during refinement, the ML error model has to be updated correspondingly, as described in Lunin & Skovoroda (1995), Urzhumtsev et al. (1996) and Afonine et al. (2005a).”
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard (2007, background): “• Location of peaks in a cross-validated likelihood-weighted difference map (Read, 1986; Urzhumtsev et al., 1996).”
Joint X-ray and neutron refinement with phenix.refine. (2010, methodology): “Usually, two maps are used to assess or rebuild the structure: cross-validated A-weighted 2mFobs DFmodel and residual mFobs DFmodel maps (Read, 1986; Urzhumtsev et al., 1996).”
Averaged kick maps: less noise, more signal…and probably less bias (2009, methodology): “The coefficients of the ML maps (Read, 1986; Pannu & Read, 1996; Murshudov et al., 1997) were computed as described in Lunin & Skovoroda (1995) and Urzhumtsev et al. (1996).”
Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules (2009, methodology): “Cross-validation has also been introduced in calculating the terms in the maximum-likelihood target function (Urzhumtsev et al., 1996).”
FEM: feature-enhanced map (2014, methodology): “…1953; Woolfson, 1956; Sim, 1959; Raman, 1959; Ramachandran & Raman, 1959; Srinivasan, 1961; Ramachandran & Srinivasan, 1961, 1970; Main, 1979; Vijayan, 1980; Urzhumtsev et al., 1996; Vellieux & Dijkstra, 1997; Read, 1997), with the most broadly used approach being A-weighted syntheses (Read, 1986).”
Likelihood-based refinement. I. Irremovable model errors. (2002, methodology): “If there exists some probabilistic hypothesis concerning the irremovable errors in the atomic model, then these parameters may be sometimes calculated explicitly [see formulae (17) and (19) below as examples; more examples are given by Urzhumtsev et al. (1996)].”