Citation for coot software how to#
The question then is how to combine these programs into a software suite, both in terms of ensuring communication between the different programs and in helping both naïve and experienced users to navigate through the suite.Įarly on in the history of CCP4, there was an agreement for all programs to use the same file formats for data files. Unsurprisingly, there is overlap of functionality, with several programs performing a particular task, albeit often using different approaches. Over the years the suite has grown continuously, with each major release featuring significant new software (see Table 1 ▶). The result is a collection of around 200 programs, ranging from large programs which are effectively packages in themselves to small ‘jiffy’ programs. While some have been commissioned by the academic committees overseeing the CCP4 project, the majority originate from the community to address a perceived gap in current functionality or to implement newly developed algorithms. Significantly, it is a collection of autonomous and independently developed programs. The CCP4 software suite is a collection of programs implementing specific algorithms concerned with macromolecular structure solution from X-ray diffraction data. While we focus here on the CCP4 software suite, we would emphasize that comparable functionality is available in other software packages such as SHARP/ autoSHARP (Vonrhein et al., 2007 ▶), SHELX (Sheldrick, 2008 ▶), ARP/ wARP (Langer et al., 2008 ▶), PHENIX (Adams et al., 2010 ▶) and many others. We intend that this article could serve as a general literature citation for the use of the CCP4 software suite in structure determination, although we also encourage the citation of individual programs, many of the relevant references for which are included here.
In this account we focus on the suite as a whole, while other articles in this issue delve deeper into individual programs. We then discuss ongoing plans for the next generation of the suite which is in development. We begin with a historical perspective on the growth of the software suite, followed by a summary of the current functionality in the suite. In this article, we give an overview of the CCP4 project, past, present and future. It encourages the wide dissemination of new ideas, techniques and practice. CCP4 aims to play a key role in the education and training of scientists in experimental structural biology. CCP4 is a community-based resource that supports the widest possible researcher community, embracing academic, not-for-profit and for-profit research. CCP4 aims to develop and support the development of cutting-edge approaches to the experimental determination and analysis of protein structure and to integrate these approaches into the CCP4 software suite.
CCP4 (Collaborative Computational Project, Num▶) exists to produce and support a world-leading integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography and other biophysical techniques.
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