Abstract
As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has produced a software framework which enables easy access to a range of programs and utilities. The resulting software suite incorporates contributions from different collaborators by encapsulating them in Python task wrappers, which are then made accessible via a user-friendly graphical user interface as well as a command-line interface suitable for scripting. The framework includes tools for project and data management. An overview of the design of the framework is given, together with a survey of the functionality at different levels. The current CCP-EM suite has particular strength in the building and refinement of atomic models into cryo-EM reconstructions, which is described in detail.
Highlights
The Collaborative Computational Project for Electron cryoMicroscopy (CCP-EM) was initiated in 2012 to support the computational needs of the macromolecular electron cryomicroscopy community
We address the CCP-EM software suite: a multi-platform suite of tools that, in time, aims to cover all aspects of cryo-EM data processing from image manipulation to the building of atomic models, and to cover multiple techniques such as single-particle reconstruction (SPR), tomography and diffraction
The CCP-EM software suite was conceived as a generic framework that could support a wide variety of functionalities, whether written by ourselves or provided by external programs
Summary
The Collaborative Computational Project for Electron cryoMicroscopy (CCP-EM) was initiated in 2012 to support the computational needs of the macromolecular electron cryomicroscopy (cryo-EM) community. The CCP-EM software suite was conceived as a generic framework that could support a wide variety of functionalities, whether written by ourselves or provided by external programs. For the many crystallographers who are interface to the associated programs Distinct from this is the moving into the cryo-EM field, the suite aims to help them mid-level management layer, which is written in pure Python. The CCP-EM This provides a bridge between the GUI layer and the third suite provides convenient pipelining and data-management layer: the set of functional programs These programs origitools, which are becoming essential as cryo-EM moves to nate from collaborating developers and are written in a wide become a high-throughput and widespread technique (Stuart variety of languages (including C, C++, Fortran and Python) et al, 2016). A full usage guide and a description of the underlying design are available in the online documentation (http:// mrcfile.readthedocs.org/)
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