Helical processing: Difference between revisions
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= Particle polishing = | = 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 = | = References = | ||
Revision as of 16:53, 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
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
[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