[3dem] RELION-5 cryo-ET pipeline
Sjors Scheres - MRC LMB
scheres at mrc-lmb.cam.ac.uk
Mon Apr 29 05:50:53 PDT 2024
Dear #teamtomo,
We are happy to announce that the new tomography pipeline in the
beta-release of RELION-5.0 is now ready for general beta-testing.
The new pipeline comprises the import of raw movie frames and MDOC
metadata files, motion correction (in RELION or UCSF MotionCor2), CTF
estimation (in CTFFIND-4.1), visual inspection of tilt series images,
tilt-series alignment (in IMOD or AreTomo), reconstruction of tomograms,
manual picking of particles in a napari-based viewer, and the extraction
of particles as 3D pseudo-subtomograms or as 2D particle stacks.
Subtomogram averaging, CTF refinement and Bayesian polishing (previously
called frame alignment) are as they were in in RELION-4.0, but the use
of 2D particle stacks considerably speeds up initial model generation,
3D classification and 3D refinement.
We hope that our definition of STAR files, with metadata required for
and generated by our pipeline, will contribute to ongoing efforts in
standardisation of the field. The upcoming CCP-EM tomography pipeline
will be based around the same definitions.
A preprint describing the pipeline is here:
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.04.26.591129v1__;!!Mih3wA!A9ZUoTtlZbfAfz3RW-Pjw_SjTMx7B153c25XH0cETzbgYYGieYNxgWb5UXOGZRaEieYdxbZwCLFJ6dcBSrN4xyVf7rI$
A detailed tutorial, including precalculated results, is here:
https://urldefense.com/v3/__https://relion.readthedocs.io/en/release-5.0/STA_tutorial/Introduction.html__;!!Mih3wA!A9ZUoTtlZbfAfz3RW-Pjw_SjTMx7B153c25XH0cETzbgYYGieYNxgWb5UXOGZRaEieYdxbZwCLFJ6dcBSrN4KDyDYDk$
RELION-5.0 remains proudly open-source, and is completely free for all
users. Download the code from:
https://urldefense.com/v3/__https://github.com/3dem/relion/tree/ver5.0__;!!Mih3wA!A9ZUoTtlZbfAfz3RW-Pjw_SjTMx7B153c25XH0cETzbgYYGieYNxgWb5UXOGZRaEieYdxbZwCLFJ6dcBSrN4S60FB6g$ and make sure you are using
version RELION-5.0-beta-3 or newer, as several important bugs have
recently been fixed.
Happy processing,
The RELION team (https://urldefense.com/v3/__https://relion.readthedocs.io/en/release-5.0/Team.html__;!!Mih3wA!A9ZUoTtlZbfAfz3RW-Pjw_SjTMx7B153c25XH0cETzbgYYGieYNxgWb5UXOGZRaEieYdxbZwCLFJ6dcBSrN44SfYOBQ$ )
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
https://urldefense.com/v3/__http://www2.mrc-lmb.cam.ac.uk/groups/scheres__;!!Mih3wA!A9ZUoTtlZbfAfz3RW-Pjw_SjTMx7B153c25XH0cETzbgYYGieYNxgWb5UXOGZRaEieYdxbZwCLFJ6dcBSrN4T0FrRJM$
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