Recent developments in the CCP-EM software suite

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.

Keywords: CCP-EM; Collaborative Computational Project for Electron cryo-Microscopy; cryo-EM.

Figure 1

Architecture of the CCP-EM software suite. The task wrappers and core libraries shown in green are written in pure Python, whereas the GUI layer is written in PyQt4. The GUI thread is independent of the job processes; task progress is monitored by a job-launch module and is recorded in an SQLite database. JSON files serve as intermediaries allowing the task to be controlled ‘headless’ without the GUI layer.

Figure 2

JSON files are used as a convenient, human-readable store of parameters and provide a consistent input for CCP-EM-supported applications. In this example, input parameters for a MOLREP job are shown, including the use of a spherically averaged phase translation function and searching for two copies of the search model in the EM volume.

Figure 3

Basic usage of the mrcfile Python library. In this example, a compressed map downloaded from the EMDB is opened and a 2 × 3 slice of data is taken from it. A new MRC file is then created, the data are copied into it and checked, and the file is closed. Finally, the file is validated to confirm that it complies with the MRC2014 standard.

Figure 4

CCP-EM project and task window. Top: CCP-EM project window showing the taskbar which is used to launch applications on the left and the project job history on the right. Bottom: example of the CCP-EM DockEM task. The toolbar at the top gives rapid access to molecular-graphics programs, job files, documentation and job launch. The input parameter setup tab is shown below, with required inputs highlighted in red. Additional launcher and results tabs appear as the job is launched and completed, respectively.

Figure 5

CCP-EM REFMAC task for the refinement and validation of atomic models in high-resolution cryo-EM maps. The single task includes the generation of structure factors from an input reconstruction, as well as the application of multiple blurring and sharpening factors. The left panel shows the CCP-EM pipeline for refinement and validation against experimental half-maps. The centre panel shows the results tab and the right panel shows the input and refined model in Coot.

Figure 6

Model-building pipeline in CCP-EM. For maps (or segments thereof) with resolutions of less than ∼5 Å and an appropriate model it is suggested to try DockEM followed by Flex-EM. For higher resolution data MOLREP and REFMAC can be used for refinement if a suitable model is available. If no model is available then Buccaneer can be used to build a model de novo. Note that for medium-resolution data sets a combination of approaches is recommended.