Helical processing: Difference between revisions
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We gain experience for helical processing in Relion using the movies and micrographs from EMDB's EMPIAR | We gain experience for helical processing in Relion using the movies and micrographs from EMDB's EMPIAR database (accession number [https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10019/ EMPIAR-10019], [https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10020/ 10020], [https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10021/ 10021], [https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10022/ 10022], [https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10031/ 10031]). The related research papers are listed below: | ||
[1] Kudryashev, Mikhail, et al. "Structure of the type VI secretion system contractile sheath." Cell 160.5 (2015): 952-962. [http://www.ncbi.nlm.nih.gov/pubmed/25723169 PubMed] | [1] Kudryashev, Mikhail, et al. "Structure of the type VI secretion system contractile sheath." Cell 160.5 (2015): 952-962. [http://www.ncbi.nlm.nih.gov/pubmed/25723169 PubMed] |
Revision as of 17:05, 6 June 2016
Our results
A paper about helical processing in Relion 2.0 is still in preparation.
Definition of helical symmetry in Relion
Usage of relion_helix_toolbox
Import coordinates
Manual picking
Template-based semi-autopicking
2D classification
Notes on 3D references
3D refinement
Mask creation
The top and bottom parts of the reconstructed helical map suffer from inaccuracies of orientations. A mask which only covers the central part might improve the overall resolution. After finding out the best values for parameters on "Mask" tab, we usually set the central Z length to 30% and increase it gradually at steps of 5% to find the largest value (<=80%, because further parts are masked out anyway) which still gives the best estimated resolution. Also it seems that wider soft edges (5~8 pixels) are useful for helices.
Particle polishing
Enable helical reconstruction and copy the number of asymmetrical units from the previous 3D refinement job. Copy the helical symmetry as well if local searches of helical symmetry have not been performed. Otherwise look into the file Refine3D/jobXXX/run_model.star
for the averaged helical symmetry at the end of the refinement:
... data_model_classes loop_ _rlnReferenceImage #1 _rlnClassDistribution #2 _rlnAccuracyRotations #3 _rlnAccuracyTranslations #4 _rlnHelicalRise #5 _rlnHelicalTwist #6 Refine3D/jobXXX/run_class001.mrc 1.000000 0.186000 0.250000 21.775977 29.410791 ...
References
We gain experience for helical processing in Relion using the movies and micrographs from EMDB's EMPIAR database (accession number EMPIAR-10019, 10020, 10021, 10022, 10031). The related research papers are listed below:
[1] Kudryashev, Mikhail, et al. "Structure of the type VI secretion system contractile sheath." Cell 160.5 (2015): 952-962. PubMed
[2] Fromm, Simon A., et al. "Seeing tobacco mosaic virus through direct electron detectors." Journal of structural biology 189.2 (2015): 87-97. PubMed
[3] Xu, Hui, et al. "Correction: Structural basis for the prion-like MAVS filaments in antiviral innate immunity." Elife 4 (2015): e07546. PubMed