Coot is a molecular-graphics application for model building and validation of biological macromolecules. It displays electron-density maps and atomic models, allowing model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. It also provides tools for model validation and interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, with tools for common tasks 'discoverable' through familiar user-interface elements or intuitive behaviour. 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 and has achieved widespread use within the crystallographic community. Coot is an interactive three-dimensional molecular-modelling program designed for the building and validation of protein structures. It facilitates the steps of the process, including initial construction of the protein chain using automatic model-building tools such as ARP/wARP, SOLVE/RESOLVE and Buccaneer. Model validation has become increasingly important with lower resolution data. Coot aims to provide access to as many of the tools required in the iterative refinement and validation of a macromolecular structure as possible. The primary design goal has been to make the software easy to learn for scientists beginning to work with X-ray data. The program is constructed from a range of existing software libraries and a purpose-written Coot library. The OpenGL and other graphics libraries, such as the X Window System and GTK+, provide the graphical user-interface functionality. The GNU Scientific Library (GSL) provides mathematical tools such as function minimizers. The Clipper and MMDB libraries provide crystallographic tools and data types. On top of these tools are the Coot libraries, which are used to manipulate models and maps and to represent them graphically. Coot provides tools for the display of three-dimensional data falling into three classes: atomic models, electron-density maps, and generic graphical objects. The user interface is designed to be easy to learn, with intuitive behaviour, familiar and consistent interfaces, and explorable interfaces. The main Coot user interface window includes a three-dimensional canvas, a menu bar, a toolbar, and a status bar. The user interface is implemented using the GTK+2 widget stack. Coot uses a lighting model that is a departure from the approach adopted in most molecular-graphics software. It uses a 'marching-cubes'-type algorithm to visualize the surface of electron-density regions higher than a chosen electron-density value. The colour of the electron-density map may be selected by the user. Difference maps are contoured at two levels, one positive and one negative. Coot displays the atoms of the atomic models as points on the three-dimensional canvas. If the points are within bonding distance, a line symbolizing a bond is drawn between the atomic points. The atoms are coloured by element, with carbonCoot is a molecular-graphics application for model building and validation of biological macromolecules. It displays electron-density maps and atomic models, allowing model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. It also provides tools for model validation and interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, with tools for common tasks 'discoverable' through familiar user-interface elements or intuitive behaviour. 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 and has achieved widespread use within the crystallographic community. Coot is an interactive three-dimensional molecular-modelling program designed for the building and validation of protein structures. It facilitates the steps of the process, including initial construction of the protein chain using automatic model-building tools such as ARP/wARP, SOLVE/RESOLVE and Buccaneer. Model validation has become increasingly important with lower resolution data. Coot aims to provide access to as many of the tools required in the iterative refinement and validation of a macromolecular structure as possible. The primary design goal has been to make the software easy to learn for scientists beginning to work with X-ray data. The program is constructed from a range of existing software libraries and a purpose-written Coot library. The OpenGL and other graphics libraries, such as the X Window System and GTK+, provide the graphical user-interface functionality. The GNU Scientific Library (GSL) provides mathematical tools such as function minimizers. The Clipper and MMDB libraries provide crystallographic tools and data types. On top of these tools are the Coot libraries, which are used to manipulate models and maps and to represent them graphically. Coot provides tools for the display of three-dimensional data falling into three classes: atomic models, electron-density maps, and generic graphical objects. The user interface is designed to be easy to learn, with intuitive behaviour, familiar and consistent interfaces, and explorable interfaces. The main Coot user interface window includes a three-dimensional canvas, a menu bar, a toolbar, and a status bar. The user interface is implemented using the GTK+2 widget stack. Coot uses a lighting model that is a departure from the approach adopted in most molecular-graphics software. It uses a 'marching-cubes'-type algorithm to visualize the surface of electron-density regions higher than a chosen electron-density value. The colour of the electron-density map may be selected by the user. Difference maps are contoured at two levels, one positive and one negative. Coot displays the atoms of the atomic models as points on the three-dimensional canvas. If the points are within bonding distance, a line symbolizing a bond is drawn between the atomic points. The atoms are coloured by element, with carbon