scispace - formally typeset
Search or ask a question
Journal ArticleDOI

EMAN2: an extensible image processing suite for electron microscopy.

TL;DR: EMAN2 has been under development for the last two years, with a completely refactored image processing library, and a wide range of features to make it much more flexible and extensible than EMAN1.
About: This article is published in Journal of Structural Biology.The article was published on 2007-01-01. It has received 2852 citations till now. The article focuses on the topics: Image processing & Python (programming language).
Citations
More filters
Journal ArticleDOI
TL;DR: Developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined are described.

4,554 citations


Cites background or methods from "EMAN2: an extensible image processi..."

  • ...Efforts to do so in APPION (Lander et al., 2009) and EMAN2 (Tang et al., 2007) are currently ongoing (personal communication with Bridget Carragher and Steven Ludtke, respectively)....

    [...]

  • ..., 2009) and EMAN2 (Tang et al., 2007) are currently ongoing (personal communication with Bridget Carragher and Steven Ludtke, respectively)....

    [...]

  • ...Second, general refinement behaviour and computational costs of the MAP optimization approach were tested using an experimental cryo-EM data set of 5168 GroEL particles that is distributed as part of a workshop on the EMAN2 software package (Tang et al., 2007)....

    [...]

Journal ArticleDOI
09 Nov 2018-eLife
TL;DR: CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations in the third major release of RELION.
Abstract: Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2-0.7 A compared to previous RELION versions.

3,520 citations


Cites methods from "EMAN2: an extensible image processi..."

  • ...In the mean time, also general-purpose programs that already existed, like EMAN2 (Tang et al., 2007), Frealign (Grigorieff, 2007) or IMAGIC (van Heel et al., 1996), were further improved and used for high-resolution structure determination....

    [...]

Journal ArticleDOI
TL;DR: The main target of Gctf is to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra of observed micrographs after background subtraction to improve CTF parameters of all particles for subsequent image processing.

2,919 citations


Cites background or methods from "EMAN2: an extensible image processi..."

  • ...CTF parameters from the text log file can also be easily extracted and used for other programs such as Frealign (Grigorieff, 2007), EMAN (Ludtke et al., 1999; Tang et al., 2007), Spider (Shaikh et al....

    [...]

  • ...There are currently several programs available for CTF determination (Ludtke et al., 1999; Mallick et al., 2005; Mindell and Grigorieff, 2003; Penczek et al., 2014; Shaikh et al., 2008; Sorzano et al., 2004; Tang et al., 2007; Vargas et al., 2013; Voortman et al., 2011)....

    [...]

  • ...CTF parameters from the text log file can also be easily extracted and used for other programs such as Frealign (Grigorieff, 2007), EMAN (Ludtke et al., 1999; Tang et al., 2007), Spider (Shaikh et al., 2008) and Xmipp (Sorzano et al., 2004) etc....

    [...]

Journal ArticleDOI
07 Jul 2016-Nature
TL;DR: It is demonstrated that the liposome-leakage and pore-forming activities of the gasdermin-N domain are required for pyroptosis and provide insights into the roles of theGasdermin family in necrosis, immunity and diseases.
Abstract: The N-terminal domains of gasdermin proteins cause pyroptotic cell death by oligomerizing to form membrane pores.

1,567 citations

Journal ArticleDOI
14 Mar 2014-Science
TL;DR: To compare the architectures and domain organization of diverse Cas9 proteins, the atomic structures of Cas9 from Streptococcus pyogenes and Actinomyces naeslundii and AnaCas9 were determined by x-ray crystallography and three-dimensional reconstructions of apo-SpyCas9, SpyCas9:RNA, and SpyCas 9:RNA:DNA were obtained by negative-stain single-particle electron microscopy.
Abstract: Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. We report 2.6 and 2.2 angstrom resolution crystal structures of two major Cas9 enzyme subtypes, revealing the structural core shared by all Cas9 family members. The architectures of Cas9 enzymes define nucleic acid binding clefts, and single-particle electron microscopy reconstructions show that the two structural lobes harboring these clefts undergo guide RNA-induced reorientation to form a central channel where DNA substrates are bound. The observation that extensive structural rearrangements occur before target DNA duplex binding implicates guide RNA loading as a key step in Cas9 activation.

1,034 citations

References
More filters
Journal ArticleDOI
TL;DR: Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales.
Abstract: The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.

35,698 citations


"EMAN2: an extensible image processi..." refers methods in this paper

  • ...For structural biology, this largely began with the visualization community, Wrst with packages like Chimera (Pettersen et al., 2004), Vision (Sanner et al....

    [...]

  • ...For structural biology, this largely began with the visualization community, Wrst with packages like Chimera (Pettersen et al., 2004), Vision (Sanner et al., 2002) and Pymol (http://pymol.sourceforge.net) which are written largely in Python with supporting libraries in C/C++....

    [...]

Book
01 Jan 1994
TL;DR: The book is an introduction to the idea of design patterns in software engineering, and a catalog of twenty-three common patterns, which most experienced OOP designers will find out they've known about patterns all along.
Abstract: The book is an introduction to the idea of design patterns in software engineering, and a catalog of twenty-three common patterns. The nice thing is, most experienced OOP designers will find out they've known about patterns all along. It's just that they've never considered them as such, or tried to centralize the idea behind a given pattern so that it will be easily reusable.

22,762 citations


"EMAN2: an extensible image processi..." refers methods in this paper

  • ...Internally, this infrastructure is implemented using several now-standard C++ programming design patterns (Gamma et al., 1995): Abstract Factories, Factory Methods and Singleton Classes....

    [...]

Journal ArticleDOI
TL;DR: IMOD is useful for studying and modeling data from tomographic, serial section, and optical section reconstructions and allows image data to be visualized by several different methods.

4,830 citations


"EMAN2: an extensible image processi..." refers background or methods in this paper

  • ...Over the last three decades, a wide range of scientiWc image processing packages have been developed for use with electron microscopy, including SPIDER (Frank et al., 1996), IMAGIC (van Heel et al., 1996), BSOFT (Heymann, 2001), FREALIGN (GrigorieV, 1998), EM (Hegerl, 1996), IMIRS (Liang et al., 2002), SUPRIM (Schroeter and Bretaudiere, 1996), IMOD (Kremer et al., 1996), PHOELIX (Carragher et al., 1996), PFT (Baker and Cheng, 1996), the MRC reconstruction tools (Crowther et al., 1996) and Xmipp (Sorzano et al., 2004)....

    [...]

  • ..., 2002), SUPRIM (Schroeter and Bretaudiere, 1996), IMOD (Kremer et al., 1996), PHOELIX (Carragher et al....

    [...]

  • ...…BSOFT (Heymann, 2001), FREALIGN (GrigorieV, 1998), EM (Hegerl, 1996), IMIRS (Liang et al., 2002), SUPRIM (Schroeter and Bretaudiere, 1996), IMOD (Kremer et al., 1996), PHOELIX (Carragher et al., 1996), PFT (Baker and Cheng, 1996), the MRC reconstruction tools (Crowther et al., 1996) and Xmipp…...

    [...]

Journal ArticleDOI
TL;DR: A novel software package called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is developed, which will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model and to facilitate structure solution for both the novice and expert crystallographer.
Abstract: Structural genomics seeks to expand rapidly the number of protein structures in order to extract the maximum amount of information from genomic sequence databases. The advent of several large-scale projects worldwide leads to many new challenges in the field of crystallographic macromolecular structure determination. A novel software package called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is therefore being developed. This new software will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model and to facilitate structure solution for both the novice and expert crystallographer.

4,201 citations


"EMAN2: an extensible image processi..." refers methods in this paper

  • ...When we began to work with the PHENIX (Adams et al., 2004, 2002) project to produce SPARX (see the companion piece in this issue), it became clear that many features necessary to take the next steps towards higher resolution reconstructions and development of novel techniques could not be reasonably incorporated into the original EMAN1 design....

    [...]

  • ...PHENIX is based on the WxPython toolkit, while EMAN1 makes use of the QT toolkit in C++....

    [...]

  • ...When we began to work with the PHE-NIX ( Adams et al., 2004, 2002 ) project to produce SPARX (see the companion piece in this issue), it became clear that many features necessary to take the next steps towards higher resolution reconstructions and development of novel techniques could not be reasonably incorporated into the original EMAN1 design....

    [...]

  • ...Current EMAN2 image display widgets use WxPython for PHENIX compatibility....

    [...]

  • ...When we began to work with the PHENIX (Adams et al., 2004, 2002) project to produce SPARX (see the companion piece in this issue), it became clear that many features necessary to take the next steps towards higher resolution reconstructions and development of novel techniques could not be…...

    [...]

Proceedings ArticleDOI
13 Jun 1988
TL;DR: The design, implementation, and performance of the Condor scheduling system, which operates in a workstation environment, are presented and a performance profile of the system is presented that is based on data accumulated from 23 stations during one month.
Abstract: The design, implementation, and performance of the Condor scheduling system, which operates in a workstation environment, are presented. The system aims to maximize the utilization of workstations with as little interference as possible between the jobs it schedules and the activities of the people who own workstations. It identifies idle workstations and schedules background jobs on them. When the owner of a workstation resumes activity at a station, Condor checkpoints the remote job running on the station and transfers it to another workstation. The system guarantees that the job will eventually complete, and that very little, if any, work will be performed more than once. A performance profile of the system is presented that is based on data accumulated from 23 stations during one month. >

2,570 citations


"EMAN2: an extensible image processi..." refers background in this paper

  • ...This separation opens the possibility of supporting other parallel computing environments like Condor (Litzkow et al., 1988) or systems similar to FoldingAtHome (Shirts and Pande, 2006) in the future, without any substantial internal changes....

    [...]