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.

Figure 1

Coot architecture, showing the layers of functionality from the user interface down to some of the low-level libraries. The libraries are described in more detail in the main text (§§3.4, 3.5, 4.3 and 4.4).

Figure 2

The Coot main window. The main display area shows a molecule and electron density. At the top of the window is a menu bar providing access to most of the tools. Commonly used model-manipulation tools are also available through the toolbar on the right. Below the menu bar is an area for user-definable buttons. A status bar is displayed below the three-dimensional canvas.

Figure 3

Mouse controls: a schematic mouse is shown with the clicked button in grey. Additional keys to be pressed are shown to the left of the mouse. On the right-hand side is a schematic of the mouse control action together with an explanation.

Figure 4

Real-space refinement of a mispositioned residue. The coloured bonds show the original structure. The white bonds show the refined atoms after dragging and refinement. The coloured boxes in the pop-up window indicate how well the new model obeys various geometric restraints. Clicking the ‘Accept’ button will cause the coloured atoms to be moved to the new positions.

Figure 5

A model with an NCS ghost. The thick bonds represent the atoms in one chain of the protein. The thin bonds represent an NCS-related chain transformed to superpose on the first chain. At the bottom of the screen the atoms coincide; at the top the main chain deviates and a side chain is in a different conformation.

Figure 6

Electron density with NCS map for the same model and in the same orientation as the previous figure. The blue density is for the original chain. The magenta contour represents the electron density for the NCS-related chain transformed back onto the original chain and clearly showing the differences.

Figure 7

A typical validation graph. Bars represent individual residues in a chain, with an indication of quality for the residue being given by both the size and colour of the bar. The plot is interactive, i.e. clicking on a bar takes the user to the corresponding residue.

Figure 8

Screenshot of a classical Ramachandran plot showing all residues, with the axes defining the ϕ and ψ angles (angles in degrees). Preferred regions are coloured in pink, allowed regions in yellow and the background in grey for disallowed regions. Standard residues are shown as dark blue squares, Pro residues as light blue squares and Gly residues as light blue open triangles. Residues in the disallowed regions are coloured red.

Figure 9

Screenshot of a Kleywegt plot (Kleywegt, 1996 ▶) showing Ramachandran differences between two NCS-related chains by connecting lines (angles in degrees). Labels, colouring and symbols are as in the previous figure. Arrows link NCS-related residues.