Recent developments in theCCP-EMsoftware suite

Abstract

As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryoMicroscopy (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.

Current approaches for the fitting and refinement of atomic models into cryo-EM maps usingCCP-EM

“…We emphasize the importance of selecting appropriate levels of map blurring/sharpening, which may be facilitated by considering the behaviour of the average map amplitude at different resolutions, and the utility of simultaneously viewing multiple blurred/sharpened maps. These tools are available from within the CCP-EM interface (Burnley et al , 2017). …”

“…An array of blurred/sharpened maps can be output by REFMAC 5 and loaded into Coot automatically using the CCP-EM GUI (Burnley et al , 2017). However, note that this is for gaining intuition by visual inspection of the maps, and that at present REFMAC 5 will only use one map with one level of blurring/sharpening when performing the actual refinement.…”

“…Plot of average structure-factor amplitude against resolution to aid the selection of the optimal blurring/sharpening B value, as shown in the CCP-EM GUI (Burnley et al , 2017). The data correspond to a cryo-EM reconstruction of β -galactosidase (PDB entry 5a1a, EMDB entry EMD-2084; Bartesaghi et al , 2015).…”

“…In this contribution, we review the tools available for macromolecular structure refinement into cryo-EM reconstructions that are available via CCP-EM (Burnley et al , 2017). Specifically, we focus on the program REFMAC 5 (Murshudov et al , 2011), noting that other refinement software and suites employ similar technologies (see, for example, Afonine et al , 2013).…”

Cryo-EM for Small Molecules Discovery, Design, Understanding, and Application

“…In crystallography, software packages such as Phenix.refine (Afonine et al, 2012), ARP/wARP (Lamzin et al, 2012) and GlobalPhasing PipeDream (Sharff et al, 2011) are designed to link and automate (in different ways and to a different extent, depending on the package) a structure solution stage, structure refinement step(s) and automated ligand fitting. While these packages are still mostly designed for use with x-ray diffraction data, modifications have been implemented to allow working with EM maps (for example CCPEM (Wood et al, 2015) (Burnley et al, 2017), Phenix CryoFit (Kirmizialtin et al, 2015) or Rosetta (Wang et al, 2016b)). Next steps should be linking these EM-specific variations into a single pipeline, which would ideally require minimal user input, and output a final model ready to be used for further drug design.…”