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Cryo-EM Software

UNIX/Linux Software

“UNIX” refers to a family of operating systems that include IRIS, Solaris, Tru64 and Linux. UNIX was designed to be a multi-user, shared, networked operating environment with concepts such as Users, Groups, Permissions and Network-Shared Resources built in to the core of its design.

The Introduction to UNIX manual is geared to beginners but is useful for novice and veteran users alike.

Here is a brief list of Linux commands that most users find helpful. Facility users and staff also recommend as a starting point for additional scripts.

Software tools for Image processing

EM analysis software is available to facility users via the SBGrid.

Full data processing requires using the ACCRE cluster. Users must register for a cluster account.

Learn more about Software Tools for Molecular Microscopy on WikiBooks.

EM Software Suite Options

RELION (for REgularised LIkelihood OptimisatioN, pronounced “rely-on”) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).  Find a brief Relion manual for data processing.

EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.

Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents a unified interface for both biologists and developers.

The cross-software GUI wrapper works with Xmipp, Relion, EMAN2 and other software suites.