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. 2021 Dec 1;77(Pt 12):1497-1515.
doi: 10.1107/S2059798321011700. Epub 2021 Nov 30.

Ten things I `hate' about refinement

Pietro Roversi  1 , Dale E Tronrud  2
Affiliations

Ten things I `hate' about refinement

Pietro Roversi et al. Acta Crystallogr D Struct Biol. .

Abstract

Macromolecular refinement is an optimization process that aims to produce the most likely macromolecular structural model in the light of experimental data. As such, macromolecular refinement is one of the most complex optimization problems in wide use. Macromolecular refinement programs have to deal with the complex relationship between the parameters of the atomic model and the experimental data, as well as a large number of types of prior knowledge about chemical structure. This paper draws attention to areas of unfinished business in the field of macromolecular refinement. In it, we describe ten refinement topics that we think deserve attention and discuss directions leading to macromolecular refinement software that would make the best use of modern computer resources to meet the needs of structural biologists of the twenty-first century.

Keywords: bias; correlations; refinement; restraints.

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Figures

Figure 1
Figure 1
Size reduction of computers over time. In (a) you can see a VAX 11/780 (picture taken in the early 1980s) and in (b) a Raspberry Pi 4 Model B sitting on the same brown logbook as is visible in (a).
Figure 2
Figure 2
Example of the validation of automatically generated stereochemical restraints. (a) An automatically generated stereochemical restraint CIF was used by Coot to idealize the coordinates of a model of the FADH2 molecule. (b) A comparison with a CPK model of FAD easily shows the flaws in this library. It is an interesting demonstration of the limitations of ‘freshman chemistry’ that it is impossible to build a CPK model of FADH2 because a serious clash created by the second H atom forces a significant distortion of the ring-system plane.
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