Abstract
The CCP4 (Collaborative Computational Project, Number 4) software suite for macromolecular structure determination by X-ray crystallography groups brings together many programs and libraries that, by means of well established conventions, interoperate effectively without adhering to strict design guidelines. Because of this inherent flexibility, users are often presented with diverse, even divergent, choices for solving every type of problem. Recently, CCP4 introduced CCP4i2, a modern graphical interface designed to help structural biologists to navigate the process of structure determination, with an emphasis on pipelining and the streamlined presentation of results. In addition, CCP4i2 provides a framework for writing structure-solution scripts that can be built up incrementally to create increasingly automatic procedures.
Highlights
CCP4 (Collaborative Computational Project, Number 4) began in 1979 as a forum for collaboration between academic macromolecular crystallography (MX) software developers
The compressed file can be reimported into another CCP4i2 database; this is performed with careful checking of consistency between the database and the unpacked project directory and using the database data item UUIDs to ensure that data are neither duplicated nor inappropriately overwritten
As an illustration of the power of the array of crystallographic functionality that has been wrapped for use in CCP4i2 as described above, we have developed a ligand pipeline that spans the entire workflow from data reduction to ligand building and automatic ligand placement to cater for the case of investigating fragment and/or drug binding to a well characterized crystal system
Summary
CCP4 (Collaborative Computational Project, Number 4) began in 1979 as a forum for collaboration between academic macromolecular crystallography (MX) software developers Today, it is best known for supporting and releasing a suite of programs (Winn et al, 2011) that have been contributed by a wide range of developers, and for organizing meetings and workshops that are geared to educating inexperienced crystallographers. CCP4i (Potterton et al, 2002), the first widely used graphical user interface (GUI) to the suite, simplified and expedited use of the suite and provided tools to view files and to track the structure-solution process in a database. A key objective for CCP4i2 is to improve accessibility for inexperienced crystallographers, enabling straightforward structure solution using a default approach, with clear reports and documentation allowing users to understand the process and investigate results. The ‘Input’ usually has several tabs, with the topmost tab being labelled ‘input data’ and allowing the user to select the
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