Shaoda He, a PhD-student in the Scheres group, implemented a workflow for the processing of helical assemblies. This involves additional tabs to the parameter-panels of the Auto-picking, Particle extraction, 2D classification, 3D classification, 3D auto-refine, Particle polishing and Mask create job-types. We do not have a separate tutorial for processing helical assemblies. The general principles remain the same as for single-particle analysis, which is covered in this tutorial. Therefore, users intending to use relion for helical processing are still encouraged to do this tutorial first. For a detailed description of the helical options, the user is referred to the corresponding pages on the RELION wiki, or to Shaoda’s paper[HS17]. We are aware that a tutorial on helical processing is probably overdue, but due to time constraints we haven’t got to doing that yet. Sorry…
Initial model generation for amyloids¶
relion_helix_inimodel2d program is a new feature in relion-3.1.
It allows generation of an initial 3D reference for helical reconstruction, in particular for amyloids.
It is run from the command line, and takes a selection of suitable 2D class averages as input.
It will try to align these class averages with respect to each other to form a continuously changing density that spans an entire cross-over.
At the heart of the iterative refinement process lies a tomographic 2D reconstruction with all 1D pixel columns from the cross-over.
Details of this program, together with a more elaborate documentation of its functionality remain to be published.
Possible usage is:
relion_helix_inimodel2d --i Select/job056/class_averages.star \ --crossover_distance 800 --angpix 1.15 --maxres 9 --search_shift 3 \ --mask_diameter 250 --j 6 --iter 5 --o IniModel/run1 relion_helix_inimodel2d --i IniModel/run1_it005.star \ --iniref 1@IniModel/run1_it005_reconstructed.mrcs --angpix 1.15 \ --maxres 6 --search_angle 2 --step_angle 0.5 --mask_diameter 250 \ --j 6 --iter 5 --o IniModel/run2
We like xmipp-2.4 for live-updated display of the following images during the optimisation:
xmipp_show -img rec.spi after_reproject.spi before_reproject.spi -poll &