A strategy for combining restrained least squares with computer graphics in the refinement of protein structures

New tools for the analysis and validation of cryo-EM maps and atomic models

“…deviation between covalent bond lengths calculated from atomic coordinates of the model and those found in restraints libraries is a global validation metric that is almost universally used in validation reports. While this metric is useful in providing an overall indication of model geometric quality, it is unlikely to reveal one or a few covalent bonds with poor geometry (Morffew & Moss, 1983;Urzhumtsev, 1992). In contrast, local metrics, for example the quality of a residue side-chain fit into the density map measured with a map correlation, or validation of (', ) torsion angles in proteins (Ramachandran et al, 1963), are good at identifying local issues, but may be voluminous and require careful presentation.…”

Crystallographic model quality at a glance

“…Reporting only the mean values of # 2009 International Union of Crystallography Printed in Singapore -all rights reserved the deviations from standard geometry, which are global model characteristics, may be insufficient (Morffew & Moss, 1983;Urzhumtsev et al, 1989;Laskowski et al, 1993); for a more complete estimation of model quality, maximal distortion values (Urzhumtsev, 1992) should also be communicated. In some ways, maximal deviations can characterize locally different kinds of geometry distortion.…”