Single-particle electron microscopy has now reached maturity, becoming a commonly used method in the examination of macromolecular structure. Using a small amount of purified protein, isolated molecules are observed under the electron microscope and the data collected can be averaged into a 3D reconstruction. Single-particle electron microscopy is an appropriate tool for the analysis of proteins that can only be obtained in modest quantities, like many of the large complexes currently of interest in biomedicine.
Permits to interactively visualize and analyse molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. UCSF Chimera allows users to incorporate new features. It contains some extensions which permits to visualize large-scale molecular assemblies such as viral coats, and allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions can be used for extend the tool capabilities.
Refines macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) data. RELION employs an empirical Bayesian approach. It can be utilized for both simulated and experimental data. This tool estimates the accuracy of alignment of individual particles and the relative contribution of the different frequencies therein. It enables the correction of per-particle defocus variations.
Permits surface rendering, multivariate statistical analysis (MSA), automatic classification, projection matching, angular reconstitution, automatic particle selection. IMAGIC can be employed for real data processing run for educational or testing purposes. This tool can exploit the properties of cheap graphic processors. It is useful for 4D analysis at atomic resolution or for refining towards multiple 3D structures.
Uses an approach based on prediction of specimen position during the tilt series from the position at previous tilts. SerialEM is a program that can acquire a variety of data from electron microscopes: tilt series for electron tomography, large image areas for 3-D reconstruction from serial sections, and images for reconstruction of macromolecules by single-particle methods. In addition to automating data acquisition, the program provides an integrated user interface for image acquisition, display, and storage.
Describes the reconstruction of biological molecules from the electron micrographs of single particles. SPIDER is an open source project that manages computation using the image-processing software and can also using a graphical user interface (GUI), termed the SPIDER Reconstruction Engine. These two approaches are described to obtain an initial reconstruction: random-conical tilt and common lines.
Reconstructs single particle from electron cryo-microscopy (cryoEM) images. EMAN is capable of processing large data sets and focuses on processing data from transmission electron microscopes. The application is mainly dedicated to single particle rebuilding but includes more than 40 functionalities allowing users to perform helical reconstruction or single particle tomography as well as interacting with external software such as Frealign or Relion.
Provides an image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. SPARX includes a graphical user interface that provides a complete graphical programming environment with a data/process-Xow infrastructure, an extensive library of Python scripts that perform speciWc TEM-related computational tasks, and a core library of fundamental C++ image processing functions. In addition, SPARX relies on the EMAN2 library and cctbx, the open-source computational crystallography library from PHENIX. The design of the system is such that future inclusion of other image processing libraries is a straightforward task. SPARX and all dependencies are free for academic use and available with complete source.