New tools for automated high-resolution cryo-EM structure determination in RELION-3

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 pytho...

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Vydané v:	eLife Ročník 7
Hlavní autori:	Zivanov, Jasenko, Nakane, Takanori, Forsberg, Björn O, Kimanius, Dari, Hagen, Wim JH, Lindahl, Erik, Scheres, Sjors HW
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	England eLife Sciences Publications Ltd 09.11.2018 eLife Sciences Publications, Ltd
Predmet:	Automation Automation, Laboratory - methods Bayesian analysis Biochemistry towards Bioinformatics biokemi med inriktning mot bioinformatik Classification Cryo-EM Cryoelectron Microscopy - methods Datasets Fourier transforms Image Processing, Computer-Assisted - methods Laboratories Microscopy Molecular biology Sensors single-particle analysis Software Structural Biology and Molecular Biophysics Tools and Resources Heidelberg Germany Sweden Stockholm Sweden United States > US Germany structural biology none software molecular biophysics Cryo-EM single-particle analysis
ISSN:	2050-084X, 2050-084X
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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 Å compared to previous RELION versions.
AbstractList	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 Å compared to previous RELION versions. 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, 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 Å compared to previous RELION versions. 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 angstrom compared to previous RELION versions. 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 Å compared to previous RELION versions.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 Å compared to previous RELION versions.
Author	Forsberg, Björn O Kimanius, Dari Zivanov, Jasenko Nakane, Takanori Hagen, Wim JH Scheres, Sjors HW Lindahl, Erik
Author_xml	– sequence: 1 givenname: Jasenko orcidid: 0000-0001-8407-0759 surname: Zivanov fullname: Zivanov, Jasenko organization: MRC Laboratory of Molecular Biology, Cambridge, United Kingdom – sequence: 2 givenname: Takanori orcidid: 0000-0003-2697-2767 surname: Nakane fullname: Nakane, Takanori organization: MRC Laboratory of Molecular Biology, Cambridge, United Kingdom – sequence: 3 givenname: Björn O surname: Forsberg fullname: Forsberg, Björn O organization: Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden – sequence: 4 givenname: Dari surname: Kimanius fullname: Kimanius, Dari organization: Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden – sequence: 5 givenname: Wim JH orcidid: 0000-0001-6229-2692 surname: Hagen fullname: Hagen, Wim JH organization: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany, Cryo-Electron Microscopy Service Platform, European Molecular Biology Laboratory, Heidelberg, Germany – sequence: 6 givenname: Erik orcidid: 0000-0002-2734-2794 surname: Lindahl fullname: Lindahl, Erik organization: Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden, Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden – sequence: 7 givenname: Sjors HW orcidid: 0000-0002-0462-6540 surname: Scheres fullname: Scheres, Sjors HW organization: MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/30412051$$D View this record in MEDLINE/PubMed https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-239781$$DView record from Swedish Publication Index (Kungliga Tekniska Högskolan) https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-207023$$DView record from Swedish Publication Index (Linköpings universitet) https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-162855$$DView record from Swedish Publication Index (Stockholms universitet)
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Snippet	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...
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SubjectTerms	Automation Automation, Laboratory - methods Bayesian analysis Biochemistry towards Bioinformatics biokemi med inriktning mot bioinformatik Classification Cryo-EM Cryoelectron Microscopy - methods Datasets Fourier transforms Image Processing, Computer-Assisted - methods Laboratories Microscopy Molecular biology Sensors single-particle analysis Software Structural Biology and Molecular Biophysics Tools and Resources
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Title	New tools for automated high-resolution cryo-EM structure determination in RELION-3
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