A real-space refinement procedure for proteins

By R. Diamond. 1971

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Citations in the corpus

Towards automated crystallographic structure refinement with phenix.refine (2012, background): “Real-space refinement (RSR) of coordinates has a long history (Diamond, 1971; Deisenhofer et al., 1985; Urzhumtsev, Lunin & Vernoslova, 1989; Jones et al., 1991; Oldfield, 2001; Chapman, 1995; see also the discussion of and references to earlier original works in Murshudov et al., 1997; Korostelev…”
Real-space refinement in PHENIX for cryo-EM and crystallography (2018, methodology): “…be optimally scaled, Assuming the target ϱtar and model-calculated ϱcalc maps are provided on the same grid, a continuous integration in (2) and (3) can be replaced with a numeric integration over the regular grid on which the maps are available (see, for example, Diamond, 1971), or respectively.”
New tools for the analysis and validation of cryo-EM maps and atomic models (2018, methodology): “Also, there exist other approaches to obtaining a map from a model (e.g., Diamond, 1971; Chapman, 1995; Sorzano et al., 2015).”
Incorporation of prior phase information strengthens maximum-likelihood structure refinement. (1998, background): “Another approach would be to carry out the re®nement in real space as suggested by Diamond (1971).”
Three-dimensional pattern recognition: an approach to automated interpretation of electron density maps of proteins. (1974, methodology): “However, this procedure still requires months of labor by one or more competent crystallographers, who must then measure the provisional atomic co-ordinates from the model and refine them further with computer programs now available (Diamond, 1966,1971; Levitt & Lifson, 1969).”
Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. (1978, methodology): “The procedure we used is different from the methods developed by Diamond (1971) or as used by Freer et aE.”
Simulated-annealing real-space refinement as a tool in model building. (2002, methodology): “Most implementations have followed Diamond (1971) in using Gaussian functions to approximate the density for each atom.”
Checking your imagination: applications of the free R value. (1996, background): “In principle, the use of real-space refinement techniques [ 37 ] could introduce some bias towards the test reflections, but the seriousness of this effect has not been demonstrated.”
X-LIGAND: an application for the automated addition of flexible ligands into electron density. (2001, methodology): “It was necessary to edit the ligand torsion angle in this example because RSTR fails to shift atoms connected by a large number of torsion angles because of correlation between these torsion angles (Diamond, 1971).”
A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent. (2001, methodology): “Real-space torsion-angle re®nement was ®rst implemented by Diamond (1971).”