While this goal has not been met for every feature, it has played a major role in many of the design decisions that have shaped the software. A primary design goal has been to make the software easy to learn in order to provide a low barrier for scientists who are beginning to work with X-ray 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 in order to facilitate those aspects of the process which cannot be performed automatically. The refinement and validation steps become increasingly important and also more time-consuming with lower resolution data. In consequence, relatively more time and emphasis is placed on model validation than has previously been the case (Dauter, 2006 ▶). In recent years, initial construction of the protein chain has often been carried out using automatic model-building tools such as ARP/ wARP (Langer et al., 2008 ▶), SOLVE/ RESOLVE (Wang et al., 2004 ▶) and more recently Buccaneer (Cowtan, 2006 ▶). Coot is an interactive three-dimensional molecular-modelling program particularly designed for the building and validation of protein structures by facilitating the steps of the process. Macromolecular model building using X-ray data is an interactive task involving the iterative application of various optimization algorithms with evaluation of the model and interpretation of the electron density by the scientist. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. 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). Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics.
COOT SOFTWARE CITE MANUAL
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. Coot is a molecular-graphics application for model building and validation of biological macromolecules.
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