Between objectivity and subjectivity

By Carl-Ivar Bränd´en, T. Jones. 1990

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “One measure of agreement between a model and a map is the model–map correlation coefficient (map CC; Brändén & Jones, 1990; Jones et al., 1991).”
Modelling dynamics in protein crystal structures by ensemble refinement (2012, unknown): “Real-space correlation coefficients ( Brändén and Jones, 1990 ) highlighted marked local improvements for flexible residues in particular ( Figure 3A ) with 11 residues improving by more than 0.1 in correlation coefficient.”
Metrics for comparison of crystallographic maps (2014, methodology): “Note that here we use the coefficient (4) to compare the whole syntheses, for example as in Read (1986) and Lunin & Woolfson (1993), while it can also be used locally (see, for example, Brändén & Jones, 1990; Kleywegt et al., 2004; Rupp, 2006; Tickle, 2012).”
New tools for the analysis and validation of cryo-EM maps and atomic models (2018, methodology): “Model-map correlation The model-map correlation coefficient (typically referred to as CC, map CC, map correlation, or real-space correlation; Brändén & Jones, 1990; Jones et al., 1991; see also an overview in Tickle, 2012 and references therein) is a metric that shows how well the model fits the…”
Crystal structure of a Cbtx–AChBP complex reveals essential interactions between snake α‐neurotoxins and nicotinic receptors (2005, methodology): “R-free is calculated for 5% of randomly selected reflections excluded from refinement. dRoot mean square deviation from ideal values, according to Engh and Huber (1991). eAccording to Branden and Jones (1990).”
Implementing an X-ray validation pipeline for the Protein Data Bank (2012, methodology): “In the mid-1980s it was first realised that crystallographic models could occasionally be significantly in error (Brändén & Jones, 1990); now, the community has finally agreed that deposition of models and data, as well as validation of both, should be mandatory for every new structure that is…”
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard (2007, methodology): “The final model obtained is analyzed for residue-based map correlation (Branden & Jones, 1990) and density at the coordinates of individual atoms, and an analysis including a summary of atoms and residues that are in strong, moderate, or weak density and out of density is provided.”