Efficient anisotropic refinement of macromolecular structures using FFT.

By G. Murshudov, A. Vagin, A. Lebedev, K. Wilson, Eleanor J Dodson. 1999

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Overview of the CCP4 suite and current developments (2011, methodology): “REFMAC5 will refine atomic coordinates and atomic isotropic or anisotropic displacement parameters (Murshudov et al., 1999), as well as group parameters for rigid-body refinement and TLS refinement (Winn et al., 2001, 2003).”
Phaser crystallographic software (2007, methodology): “A similar sphericity restraint is used in SHELXL (Sheldrick, 1995) and in REFMAC5 (Murshudov et al., 1999).”
Integrating model simulation tools and cryo‐electron microscopy (2022, methodology): “Atomic B-factors can be calculated from cryo-EM maps by multiple methods; cryo-EM maps can be converted into structure factors and B-factors can be calculated as they would be in an x-ray crystallography experiment.(223) Alternatively, many packages calculate B-factors in real space, by optimizing t”
Activation of a vinculin‐binding site in the talin rod involves rearrangement of a five‐helix bundle (2004, methodology): “The model of talin 482–655 was built using XtalView (McRee, 1999) and refinement carried out using REFMAC5 (Murshudov et al, 1999).”
From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation (2018, background): “As discussed in the literature (see, for example, Dunitz & White, 1973; Murshudov et al., 1999; Winn et al., 2001), the atomic displacement is a superposition of various motions that arise from different sources.”
Structural Dynamics of the Cereblon Ligand Binding Domain (2015, methodology): “The structures were finalized by cyclic manual modeling with Coot [18] and refinement with REFMAC5 [19].”