Current developments in <i>Coot</i> for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data

TLDR

Coot is a widely used tool for model building, refinement, and validation of macromolecular structures, originally developed for crystallography and now adapted to routinely handle cryo‑EM maps at 2.5–4 Å resolution, though building into such maps remains time‑consuming and requires substantial expertise. The authors aim to simplify and expedite model building in Coot by adding new tools and to present the current state‑of‑the‑art usage. New features include morphing, Geman‑McClure restraints, full‑chain refinement, and Fourier‑model based residue‑type‑specific Ramachandran restraints.

Abstract

Abstract Coot is a tool widely used for model building, refinement, and validation of macromolecular structures. It has been extensively used for crystallography and, more recently, improvements have been introduced to aid in cryo‐EM model building and refinement, as cryo‐EM structures with resolution ranging 2.5–4 A are now routinely available. Model building into these maps can be time‐consuming and requires experience in both biochemistry and building into low‐resolution maps. To simplify and expedite the model building task, and minimize the needed expertise, new tools are being added in Coot . Some examples include morphing, Geman‐McClure restraints, full‐chain refinement, and Fourier‐model based residue‐type‐specific Ramachandran restraints. Here, we present the current state‐of‐the‐art in Coot usage.