Eman semiautomated software for high-resolution single-particle reconstruction

The goal of this project is to provide software capable of performing single particle reconstructions beyond 10 a as such high resolution data become available. Singleparticle reconstruction spr and electron crystallography ec, two. In this chapter, some specialized applications are described in which computers are essential for manipulating and enhancing images obtained by using a transmission electron microscope, particularly to understand the tertiary and quaternary structures of biological macromolecules and their complexes. We present eman electron micrograph analysis, a software package for performing semiautomated singleparticle reconstructions from transmission electron micrographs. Singleparticle 3d reconstruction from cryoelectron. Workflow scheduling is one of the key issues in the management of workflow execution. To verify the feasibility and advantages of the method, two octahedral symmetrical macromolecules, that is, heat shock protein for high resolution refinement in single particle processing steve ludtke asst. This is a brief account of the earlier history of singleparticle cryoem of. Nearatomic resolution using electron cryomicroscopy and.

Baldwin, and wah chiu verna and marrs mclean department of biochemistry, national center for macromolecular imaging, baylor college of medicine. Aug 17, 2010 the reconstruction process is quite computationally intensive, and several software packages are available for this task. Highresolution single particle analysis from electron cryo jove. Previous structural studies of membrane fusion proteins have largely used crystallography of static molecular fragments, in isolation of their transmembrane domains. Ive heard that insert favorite program runs much faster than eman. Flexible filamentous virus structures from fiber diffraction volume 23 issue 2 gerald stubbs, amy kendall, michele mcdonald, wen bian, timothy bowles, sarah baumgarten, ian mccullough, jian shi, phoebe stewart, esther bullitt, david gore, said ghabrial. Conformational reorganization of the sars coronavirus. We describe a collection of standardized image processing protocols for electron microscopy singleparticle analysis using the xmipp software package. Nov 23, 2001 eman is a singleparticle analysis software package, which was first publicly distributed in 2000. Correcting for the ewald sphere in highresolution single. Probabilistic initial 3d model generation for singleparticle cryo. Highresolution single particle analysis from electron cryomicroscopy images using sphire. These data will have a very high signalto average is known, each class average is simply noise ratio at low resolution, but contain little or no inserted into the fourier volume in the correct usable highresolution information.

Spider image processing for singleparticle reconstruction of. In this article, we develop an experimental system superdragon for evaluating acceleration of a single particle cryoelectron microscopy cryoem 3d reconstruction package eman through a hybrid of cpu, gpu, and fpga parallel architecture. Reconstructs single particle from electron cryomicroscopy cryoem images. We used cryoelectron microscopy and single particlebased helical image analysis to determine the structure of the helical nucleocapsid formed by the folded domain of the measles virus nucleoprotein encapsidating an rna at a resolution of 4. Symmetrymismatch reconstruction of genomes and associated. Jan 01, 2007 eman is a scientific image processing package with a particular focus on single particle reconstruction from transmission electron microscopy tem images. Nearatomic cryoem structure of the helical measles virus. Low cost, high performance gpu computing solution for atomic. However, i would be very happy if you could provide any additional paperinformationlink to get an easier entrance in the functionality of eman 2 and single particle reconstruction. This protocol describes the reconstruction of biological molecules from the electron micrographs of single particles. 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. It was first released in 1999, and new versions have been released typically 23 times each year since that time. Support for all pointgroup symmetries including all platonic solids icosahedral, octahedral, and tetrahedral symmetries, dihedral symmetry dn, cyclic. Single particle analysis is a group of related computerized image processing techniques used to analyze images from transmission electron microscopy tem.

Structural basis of amino acid surveillance by higherorder trnamrna interactions. We demonstrate that the singleparticle reconstruction, xray scattering data and xray crystal structure all agree well at this resolution. Image processing for electron microscopy singleparticle. Pdf a framework to refine particle clusters produced by eman. Semiautomated software for highresolution singleparticle. Singleparticle refinement and variability analysis in. Reconstruction quality improves with increasing numbers of input projections that span all possible views. A refined singleparticle reconstruction procedure to process two. While the overall conformation of this structure is quite consistent with the published xray data, a measurable shift in the positions of three. Eman s focus is on providing state of the art single particle reconstruction methods automated to the greatest extent possible. Single particle reconstruction software 93 this model was then refined against the complete a graphical user interface is provided to allow rapid data set with ctf correction. Semiautomated software for highresolution singleparticle reconstructions. 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.

Singleparticle reconstruction is a methodology whereby transmission. Eman s original purpose was performing single particle reconstructions 3d volumetric models from 2d cryoem images at the highest possible resolution, but the suite now also offers support for single particle cryoet, and tools useful in many other subdisciplines such as helical reconstruction, 2d crystallography and wholecell tomography. Singleparticle reconstruction software 87 simple method. A complete singleparticle reconstruction algorithm is implemented. If you say there are no methods papers i will work through the single particle reconstruction tutorial to answer the question of usability. This protocol explains how to perform an initial low resolution reconstruction using eman. The chapter must be read with some knowledge of the basic principles of. The reconstruction approach shown here is called tomography, meaning that 2d slices of a 3d object are reconstructed. Single particle reconstruction and validation using bsoft. Eman2 has been under development for the last two years, with a completely refactored image processing library, and a wide. Oct 30, 2008 this protocol describes the reconstruction of biological molecules from the electron micrographs of single particles. Eman is one of the most popular software packages for single particle reconstruction. Multiresolution mapem method for 3d reconstruction of symmetrical particles with electron microscopy. Single particle electron microscopy em reconstruction has recently become a popular tool to get the threedimensional 3d structure of large macromolecular complexes.

Single particle electron microscopy reconstruction of the exosome complex using the random conical tilt method. Jun, 2017 the resolution and accuracy of the 3d images obtained with single particle reconstruction spr highly depend on the number and signal to noise ratio of the particle images. Li s, su z, lehmann j, stamatopoulou v, giarimoglou n, henderson fe, fan l, pintilie gd, zhang k, chen m, ludtke sj, wang yx, stathopoulos c, chiu w, zhang j. It is now possible in many cases to produce nearatomic resolution structures, and yet 23 of published structures remain at substantially lower. We present here a reconstruction, obtained by using recently developed image processing methods, of the rotavirus inner capsid particle doublelayer particle or dlp at a resolution suitable for interpretation by an atomic model. Semiautomated software for high resolution single particle reconstructions steven j. Were upgrading the acm dl, and would like your input. A method for threedimensional 3d reconstruction of macromolecule assembles, that is, octahedral symmetrical adapted functions osafs method, was introduced in this paper and a series of formulations for reconstruction by osaf method were derived. We attempt to refine the particle clusters by more accurately determining orientations of particles, and thereby achieving higher resolutions of consequent 3d structures. We use the proc2d in the eman 8 package to change the image format from gatan digital image to spider image format. Liu and cheng used cryoelectron microscopy of cypovirus particles to catch the dsrnas in the act of being copied.

Compared to xray crystallography, it has some unique advantages. Cryoem shows the polymerase structures and a nonspooled. The result establishes singleparticle reconstruction as a highresolution technique. Scheduling is a process that maps and manages execution of interdependent tasks on distributed resources. We attempt to refine the particle clusters by more accurately determining orientations of particles, and thereby achieving higher resolutions of consequent 3d. Moving on to 3d reconstruction, most importantly, the spatial. Eman is a scientific image processing package with a particular focus on single particle reconstruction from transmission electron microscopy tem images. In this protocol, we describe our practice in getting the 3d reconstruction. The goal is to permit even novice users to be able to reconstruct macromolecular structures with high veracity and at high resolution. Em projection images is challenging due to the low snr. In the bsoft version, the standard interpolation procedure with weight w 1.

Inside the host cell, the coat remains intact, and the dsrnas have to replicate within the coat. This protocol requires that the viral capsid is icosahedral and has been reconstructed at a high resolution from cryoem images of virus particles, of which the orientations and centers used for the capsid reconstruction have been determined by virus reconstruction software packages, for example, relion scheres 2012, eman ludtke et al. Spring is a singleparticle based helical reconstruction package and has been used to determine 3d structures of a variety of highly. Generalized singleparticle cryoem a historical perspective. We present eman electron micrograph analysis, a software package for performing semiautomated single particle reconstructions from transmission electron micrographs. We present a threedimensional reconstruction of native naked groel to. The sars coronavirus sarscov spike is the largest known viral spike molecule, and shares a similar function with all class 1 viral fusion proteins. Single particle electron microscopy reconstruction of the. Options are available to generate an initial model for particles with no. Standard singleparticle reconstruction methodologies in.

Seeing groel at 6 a resolution by single particle electron. Flexible filamentous virus structures from fiber diffraction. A reasonable representation of the original object, a collection of three disks, is already obtained from nine projections. These methods were developed to improve and extend the information obtainable from tem images of particulate samples, typically proteins or other large biological entities such as viruses. Computation here is performed using the imageprocessing software spider and can be managed using a graphical user interface, termed the spider reconstruction engine. Software tools for molecular microscopygeneral packages. Eman is one of the easier to master software suites for single particle analysis.

Eman is capable of processing large data sets and focuses on processing data from transmission electron microscopes. In this study we have produced purified, irradiated sarscov. Hong zhou a, b, c, a hefei national laboratory for physical sciences at nanoscale, and university of science and technology of china, hefei 230027, china. In the eman version, any of its various builtin interpolation procedures can be used. The boxed particles are used to generate a preliminary model, which is then re. Vinothkumar, richard henderson skip to main content accessibility help we use cookies to distinguish you from other users and to provide you with a. While there have been many improvements over the years, the fundamental methodology used in eman2 is the same one thats described in these papers. Dec 01, 1999 we present eman electron micrograph analysis, a software package for performing semiautomated single particle reconstructions from transmission electron micrographs.

Professor, biochemistry, bcm codirector,ncmi ncrr single particle reconstruction. Eman is a singleparticle analysis software package, which was first publicly distributed in 2000. The genomes of doublestranded rna dsrna viruses consist of about a dozen dsrna segments enclosed by a protein coat. Asymmetric reconstruction of structures with mixed symmetries. Cryoem singleparticle reconstruction has been growing rapidly over the last 3 years largely due to the development of direct electron detectors, which have provided data with dramatic improvements in image quality. Semiautomated software for high resolution single particle reconstructions, journal of structural biology on deepdyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips. By continuing to use our website, you are agreeing to our use of cookies. In single particle 3d reconstruction, an essential step is to correctly assign the proper orientation of each single particle. Based on a comprehensive workload characterization, we exploit multigrained parallelism in the cryoem 3d. Spider image processing for singleparticle reconstruction. We demonstrate that the singleparticle reconstruction, xray scattering data and xray crystal structure all agree well at this. In this article, we develop an experimental system superdragon for evaluating acceleration of a singleparticle cryoelectron microscopy cryoem 3d reconstruction package eman through a hybrid of cpu, gpu, and fpga parallel architecture. We use cookies to make interactions with our website easy and meaningful, to better understand the use of our services, and to tailor advertising.

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. Low cost, high performance gpu computing solution for atomic resolution cryoem single particle reconstruction xiaokang zhang, a, b xing zhang, b, c and z. After all the data are added to the reconstruction 3d ft. Figure 4 shows the analysis of the results and provides instructions to results after zero to three refinement iterations. Multiresolution mapem method for 3d reconstruction of.

Software tools for molecular microscopy wikibooks, open. But the particle clusters produced during its model we use cookies to enhance your experience on our website. But the particle clusters produced during its model refining stage are of low qualities. The goal of this project is to provide software capable of performing singleparticle reconstructions beyond 10 a as such highresolution data become available. We present a reconstruction of native groel by electron cryomicroscopy cryoem and single particle analysis at 6 a resolution. There are several methods to assign the view for each particle, including the angular reconstitution 1 and random conical tilt rct method 2. May 15, 2008 we describe a collection of standardized image processing protocols for electron microscopy single particle analysis using the xmipp software package. Threedimensional reconstruction by chahines method from. Eman2 has been under development for the last two years, with a completely refactored. Eman strives for the best, most accurate solution, not the fastest solution. There has been enormous progress during the last few years in the determination of threedimensional biological structures by single particle electron cryomicroscopy cryoem, allowing maps to be obtained with higher resolution and from fewer images than required previously. While several excellent software packages exist that allow singleparticle and other reconstruction procedures to be performed frank et al.