Tools for ligand validation in Coot

TLDR: The current tools of Coot for ligand validation and comparison in are presented and the user-selected ligand is assessed by ligand-distortion and map-correlation metrics, and compared with those of ligands of the wwPDB to create a percentile rank.

Abstract: Coot is a molecular-graphics program primarily aimed at model building using X-ray data. Recently, tools for the manipulation and representation of ligands have been introduced. Here, these new tools for ligand validation and comparison are described. Ligands in the wwPDB have been scored by density-fit, distortion and atom-clash metrics. The distributions of these scores can be used to assess the relative merits of the particular ligand in the protein–ligand complex of interest by means of `sliders' akin to those now available for each accession code on the wwPDB websites.