The CCP4 suite: integrative software for macromolecular crystallography.

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.

CCP4i2: the new graphical user interface to the CCP4 program suite.

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.

Potential of chlorophyll-rich feed ingredients to improve detection of fecal contamination in the abattoir.

The use of fecal fluorescence to improve detection of contamination of carcasses in the abattoir was previously reported. However, incidents of false negatives can result when animals are offered diets that contain little chlorophyll (e.g., concentrate). Here, we investigated the potential of incorporating a high-chlorophyll-containing feed ingredient (concentrated alfalfa extract; CAE) into the diets of sheep and cattle to improve fecal fluorescence intensity. The sheep experiment evaluated the fecal fluorescence of animals from pasture, when fed a concentrate-barley straw diet and when the concentrate diet incorporated CAE (100 g of dry matter a day). Fecal chlorophyll and metabolite content was highest on the pasture-fed animals and increased significantly over the concentrate diet when CAE was included. Subsequently fluorescent intensity was increased from 15,000 to 36,000 arbitrary units for concentrate and CAE-concentrate diets, respectively, compared with 59,000 for the pasture-fed animals. The cattle experiment investigated the potential of CAE to improve fluorescence of feces from a concentrate diet as well as a silage diet at two levels of incorporation (75 and 150 g CAE/kg of dry matter intake). This study also determined the fluorescence of digesta and carcass contamination in the abattoir on a subset of carcasses. In agreement with the sheep study, CAE significantly improved fluorescence of feces and digesta when added to a concentrate diet, but had little effect on improving fecal fluorescence from the silage-fed animals. This was thought to be related to greater chlorophyll degradation in the rumen or/and the dark nature of the silage feces acting as a quencher of emitted fluoresced light. Incorporating high-chlorophyll-containing plant ingredients into ruminant concentrate diets will improve detection of fecal contamination by reducing false-negative readings. However, they will have little effect on false-positive readings due to the range of wavelengths emitted by natural chlorophyll and its metabolites. Implications and potential solutions for this are discussed.

Overview of the CCP4 suite and current developments.

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.