The CCP4 (Collaborative Computational Project, Number 4) software suite is a collection of programs and associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography. The suite is designed to be flexible, allowing users a number of methods of achieving their aims. The programs are from a wide variety of sources but are connected by a common infrastructure provided by standard file formats, data objects and graphical interfaces. Structure solution by macromolecular crystallography is becoming increasingly automated and the CCP4 suite includes several automation pipelines. After giving a brief description of the evolution of CCP4 over the last 30 years, an overview of the current suite is given. While detailed descriptions are given in the accompanying articles, here it is shown how the individual programs contribute to a complete software package.

One of the most important aspects of macromolecular structure refinement is the use of prior chemical knowledge. Bond lengths, bond angles and other chemical properties are used in restrained refinement as subsidiary conditions. This contribution describes the organization and some aspects of the use of the flexible and human/machine-readable dictionary of prior chemical knowledge used by the maximum-likelihood macromolecular-refinement program REFMAC5. The dictionary stores information about monomers which represent the constitutive building blocks of biological macromolecules (amino acids, nucleic acids and saccharides) and about numerous organic/inorganic compounds commonly found in macromolecular crystallography. It also describes the modifications the building blocks undergo as a result of chemical reactions and the links required for polymer formation. More than 2000 monomer entries, 100 modification entries and 200 link entries are currently available. Algorithms and tools for updating and adding new entries to the dictionary have also been developed and are presented here. In many cases, the REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.

The CCP4 molecular-graphics program now uses the Qt framework to provide a modern look and feel. There are many new features including rendering for publication-quality images and sequence alignment.

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.

The X-ray laboratory at the University of North Carolina has been operating in its current format for over 15 years. In that time, structures have been determined using a variety of instruments, computer platforms and software packages. The data collection capabilities have expanded from dozens per year to hundreds per year and can only continue to increase. The result has been a volume of completed structures, many of which have not yet been published or deposited in the public databases. Over the years the computer data files have been saved, but little attempt, other than a reference number, has been made to allow users to search for old structures. This paper describes a project to save and categorize this data while the volume is still manageable, and provide a mechanism for future structures to be archived automatically. The main archive is a relational database with the choice of content based largely on the IUCr core CIF dictionary [1] augmented by a number of local fields. As a result, enough information is retained for each structure to permit the extraction of information required by journals with the most rigorous requirements. The main archive is only directly accessible to the system administrator and user access is via a software interface which exposes most of the database fields and a number of utilities that are based largely on the NRCVAX [2] software package. This permits the implementation of a security system which allows users to limit access to their structures as well as protecting the database from unauthorized or undocumented modification. As part of the archiving process a structure is passed through a validation procedure, similar to those employed by journals and public databases, which ensures consistency of the data and compares value ranges with those expected from a normal structure. This procedure also computes a number of fields that may be required, but are not normally produced by software, In order for the deposition to be finalized the user has either to correct any potential errors or provide an explanation which is stored with the entry. This ensures that if this structure is required at some point in the future for publication it will either pass any journal checks or the reason why not will be readily available. A number of tables are also generated that permit easy searching of the database for structures based on a number of structural or chemical criteria. The results of such a search permit an authorized user to extract the data for a structure. Utilities are provided to analyse such a structure and produce tables and graphics suitable for publication or inclusion in talks or presentations.[1] IUCr, (October 2003) http://www.iucr.org/iucrtop/cif/cif_core/index.html [2] Gabe, E