Features and development of Coot

Abstract

Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.

Intraflagellar transport proteins 172, 80, 57, 54, 38, and 20 form a stable tubulin‐binding IFT‐B2 complex

“…The first round of automatic building was performed with AutoBuild in PHENIX and resulted in 75–90% complete models. These partial models were subsequently used for molecular replacement with the native datasets and the structures finished by iterative cycles of model building in Coot (Emsley et al , 2010) and refinement in PHENIX. The structures of Mm IFT52N and Mm IFT54CH were determined by molecular replacement using the previously determined structures of Cr IFT52N and Cr IFT54CH.…”

The atomic structure of a eukaryotic oligosaccharyltransferase complex

“…The model of Stt3 was split into a transmembrane domain and a periplasmic domain. These models were docked into the 3.5-Å EM map in COOT and Chimera 50,51 . All other subunits of OST were manually built into the remaining density in the program COOT.…”

Two distinct conformational states define the interaction of human RAD 51‐ ATP with single‐stranded DNA

“…A full‐length model for human RAD51 was built, using PDB entry 1SZP for the RAD51 N‐terminal domain and 1N0W for modelling hRAD51's interdomain linker sequence. The structure was refined in Phenix (Adams et al , 2002) to a resolution of 3.9 Å, using Coot (Emsley et al , 2010) for model building and applying NCS restraints to the ATPase and N‐terminal domains of the 14 hRAD51 molecules in the asymmetric unit.…”