Single particle analysis software tools | Cryo-electron microscopy
Single particle electron microscopy is a versatile technique for the structural analysis of protein complexes in near-native conditions. While tremendous progress has been made during the past few decades in techniques for specimen preparation, imaging, and image analysis, the field is still in development.
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.
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.
Calculates and refines three-dimensional (3D) structures of macromolecular assemblies that are calculated from images collected on an electron microscope. Frealign provides a fast and accurate projection matching algorithm, and calculates 3D reconstructions that are fully corrected for the contrast transfer function (CTF) of the microscope. Other features include refinement of microscope defocus and magnification, correction for the Ewald sphere curvature, processing of helical particles, 3D classification, and density masking. Furthermore, algorithms and run scripts were developed to take advantage of parallel computing environments to speed up processing.
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.
Provides a movie alignment program. Unblur is a standalone software that evaluates per-frame shifts for each particle. The application is based on iterative alignments of each raw frame to the current best total sum of all other frames with a procedure to reduce sensitivity to noise. It also allows users to ignore filtering or to filter frame sums by the depicted exposure filter.
A tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger is useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.