On the handling of atomic anisotropic displacement parameters

By R. Grosse-Kunstleve, Paul D. Adams. 2002

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Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “Most of the modules are available through the open- source CCTBX libraries (Grosse-Kunstleve & Adams, 2002; Grosse-Kunstleve et al., 2002).”
Phaser crystallographic software (2007, background): “The anisotropic displacement ellipsoid must remain invariant under the application of each symmetry operator of the space group or site-symmetry group, respectively (Giacovazzo, 1992; Grosse-Kunstleve & Adams, 2002).”
X-ray structure determination at low resolution (2009, methodology): “To do this, the U tensor is converted into Cartesian coordinate space U cart (Grosse-Kunstleve & Adams, 2002).”
Version 1.2 of the Crystallography and NMR system (2007, methodology): “To do this, the U tensor is converted into Cartesian coordinate space U cart (see ref”
FEM: feature-enhanced map (2014, methodology): “Typically, map values are stored as a set of four-byte or eight-byte real values (eight bytes in cctbx; Grosse-Kunstleve & Adams, 2002; Grosse-Kunstleve et al., 2002), which means that having more than one or two maps simultaneously in memory may be prohibitive.”
Q|R: quantum-based refinement. (2017, methodology): “Q|R uses the cctbx open source library (Grosse-Kunstleve & Adams, 2002; Grosse-Kunstleve et al., 2002) to construct a standard refinement protocol, very much like phenix.refine and most other PHENIX tools. cctbx is used to compute the data term in (1) and its derivatives, perform scaling and…”
New tools for the analysis and validation of cryo-EM maps and atomic models (2018, methodology): “The CCTBX software library (Grosse-Kunstleve & Adams, 2002) was used to extract files from databases, compute, process and accumulate statistics.”
Bulk-solvent and overall scaling revisited: faster calculations, improved results (2013, background): “…anisotropic scale factor is defined as kanisotropic ¼ expð 2 2stUcrystsÞ; ð6Þ where Ucryst is the overall anisotropic scale matrix equivalent to U* defined in Grosse-Kunstleve & Adams (2002); st = (h, k, l) is the transpose of the Miller-index column vector s. Usón et al. (1999) define a…”