Improved Fourier Coefficients for Maps Using Phases from Partial Structures with Errors

By Randy J. Read. 1986

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Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “…Bricogne & Irwin, 1996; Murshudov et al., 1997; Adams et al., 1997; Pannu et al., 1998) the calculation of the ML target (Lunin & Urzhumtsev, 1984; Read, 1986, 1990; Lunin & Skovoroda, 1995) requires an estimation of model error parameters, which depend on the current atomic parameters and…”
Using SAD data in Phaser (2011, neutral): “For singletons (acentric reflections for which only one of F + or F À has been measured) and centric reflections, phase information comes essentially from the real scattering of the anomalous scatterer model and is computed in the same way as phase probabilities for any partial models (Read, 1986).”
Real-space refinement in PHENIX for cryo-EM and crystallography (2018, methodology): “In cryo-EM the map is a 3D reconstruction, while in crystallography it may be, for example, a 2mFobs - DFmodel map (Read, 1986).”
Experimental assessment of differences between related protein crystal structures. (1999, methodology): “Although the effect of model bias can be suppressed to some extent through the calculation of A maps (Read, 1986) or simulated-annealing omit maps (Hodel et al., 1992), it remains to be established if these methods are suf®ciently powerful for the present purpose.”
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).”
Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. (2004, methodology): “5.4. logrA and overall Luzzati Bimpf The value of log A (Srinivasan, 1966; Read, 1986) and of the overall Luzzati imperfection, Bimpf, are obtained by computing, respectively, the intercept and slope of the linear regression in d*2, 1=2 log hF2xpcti=hF2obsi d 2 log A 1=4 Bimpfd 2: 31 The values of…”
Simple algorithm for a maximum-likelihood SAD function. (2004, methodology): “Map correlation compared the ®gure-of-merit-weighted map from experimental phasing with the ®gure-of-merit-weighted SIGMAA (Read, 1986) map calculated with phases from the ®nal model.”
FEM: feature-enhanced map (2014, methodology): “In the test cases shown, the maps produced in this way are found to have increased interpretability and decreased model bias compared with the starting 2mFobs DFmodel A-weighted map.”
Metrics for comparison of crystallographic maps (2014, methodology): “Syntheses such as wFobs or 2mFobs DFcalc scaled in have both positive and negative values.”
DNA-bound structures and mutants reveal abasic DNA binding by APE1 DNA repair and coordination (2000, background): “28 ) and electron density for the DNA was clearly visible in σA-weighte”
Computational Methods for RNA Structure Validation and Improvement. (2015, methodology): “is either the real-space correlation coefficient or the real-space residual (RSR) measured as the agreement between the “experimental” electron density (usually 2mFobs DFcalc; Read, 1986) and the purely modelcalculated Fcalc electron density, within a mask around the atoms in that residue ( Jones, Z”
Detecting outliers in non-redundant diffraction data. (1999, methodology): “Data can readily be normalized by computing the Wilson parameter N for resolution shells, as performed in the program SIGMAA (Read, 1986).”