PubMed · 11163727
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J L Carrascosa, S Hovmoeller. 2001. Editorial.. https://doi.org/10.1016/s0968-4328(00)00098-6
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A review is given of the mathematical procedures required for a molecular-replacement structure determination. These apply equally to the more frequently encountered situations where a known homologous structure can be used as a search model and to phase determination in the presence of non-crystallographic symmetry (NCS). In general, the former represents improper NCS between two different unit cells, whereas the latter occurs when there is proper NCS within one unit cell.
In molecular replacement, a model, described as a list of orthogonal coordinates, is to be moved into a new position and orientation. The orthogonal coordinate system also has to be related to the crystallographic system, which may not be orthogonal, and crystallographic symmetry must be considered, which applies to coordinates expressed as fractions of the unit cell. Elementary properties of rotation matrices and their representation as polar or Eulerian angles are discussed.
An account is given of the molecular replacement method as implemented in the package AMoRe. The overall strategy of the method is presented and the main functions used in the package are described. The most important features of AMoRe are the quality of the fast rotation and translation functions and the facility of multiple inputs to translation and rigid-body refinement functions, which allow for a fast multiple exploration of crystal configurations with a high level of automation.