Skip to main page content
U.S. flag

An official website of the United States government

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Apr 1;77(Pt 4):403-410.
doi: 10.1107/S2059798321001856. Epub 2021 Mar 30.

Using RELION software within the Scipion framework

Grigory Sharov  1 , Dustin R Morado  2 , Marta Carroni  2 , José Miguel de la Rosa-Trevín  2
Affiliations

Using RELION software within the Scipion framework

Grigory Sharov et al. Acta Crystallogr D Struct Biol. .

Abstract

Scipion is a modular image-processing framework that integrates several software packages under a unified interface while taking care of file formats and conversions. Here, new developments and capabilities of the Scipion plugin for the widely used RELION software package are presented and illustrated with an image-processing pipeline for published data. The user interfaces of Scipion and RELION are compared and the key differences are highlighted, allowing this manuscript to be used as a guide for both new and experienced users of this software. Different on-the-fly image-processing options are also discussed, demonstrating the flexibility of the Scipion framework.

Keywords: RELION; Scipion; cryo-EM; image processing; single-particle analysis.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Comparison of the 3D auto-refine protocol GUIs in RELION (a) and Scipion (b). Advanced protocol parameters in Scipion are highlighted with a gray background.
Figure 2
Figure 2
The plugin for the RELION software package provides interactive wizards to help users choose optimal parameters. The arrow in (a) indicates the wizard button that launches a histogram plot (b) with an estimated number of CTF groups given the input defocus range.
Figure 3
Figure 3
Scipion offers a rich viewing interface for both item sets and individual images. (a) RELION STAR-file metadata can be sorted and plotted in various ways. (b) Individual images can be analyzed and processed with built-in ImageJ tools. Here, an interactive wizard for 2D mask design is depicted.
Figure 4
Figure 4
Simplified flow chart of RELION processing within the Scipion framework for the EMPIAR-10389 data set. We first processed the single-shot data set separately and then used the resulting map for the reference-based particle picking of both single-shot and multi-shot data sets (see the text for details). At this point the two data sets were joined and processed further together. For comparison, see Supplementary Fig. S2 in Righetto et al. (2020 ▸) and the supporting information to this manuscript.
Figure 5
Figure 5
Final results produced by the Scipion plugin for the RELION software package. (a) The cryo-EM map filtered and colored by local resolution. The scale bar is 20 Å in length. (b) Fourier shell correlation curves between the half-maps.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Bharat, T. A. M., Russo, C. J., Löwe, J., Passmore, L. A. & Scheres, S. H. W. (2015). Structure, 23, 1743–1753. - PMC - PubMed
    1. Biyani, N., Righetto, R. D., McLeod, R., Caujolle-Bert, D., Castano-Diez, D., Goldie, K. N. & Stahlberg, H. (2017). J. Struct. Biol. 198, 124–133. - PubMed
    1. Burnley, T., Palmer, C. M. & Winn, M. (2017). Acta Cryst. D73, 469–477. - PMC - PubMed
    1. Danev, R., Yanagisawa, H. & Kikkawa, M. (2019). Trends Biochem. Sci. 44, 837–848. - PubMed
    1. Grant, T., Rohou, A. & Grigorieff, N. (2018). eLife, 7, e35383. - PMC - PubMed

MeSH terms