Processing notes for Type II Amyloid-beta dataset:

Images were imported (job001), motioncorrected (job016),ctfFind(job022).
Filaments were manupicked (job025), extracted with box size 480 and classified by Class2D (job027). Majority classes are Type II ABeta42. Select all the classes (job042).
The images reprocessed with estimated gain, so motioncorrected (job052),ctfFind(job056).
Extracted all the type II particles for refinement (job057)
3D autorefine was applied with reference map userdata/DLB_0p73.mrc (job058) in this dataset.
{#for training purpose, you also can use relion_helix_inimodel2d to generate an intial model with:
relion_helix_inimodel2d --i Select/job081/class_averages.star --o IniRef/run1 --angpix 2.19 --crossover_distance 290 --iter 5 --maxres 10 --j 8
relion_image_handler --i IniRef/run1_class001_rec3d.mrc --o IniRef/run1_class001_rec3d_work.mrc --angpix 2.19 --rescale_angpix 0.73 --new_box 256 --force_header_angpix 0.73}
The particles were polished (job071) and ctfrefined (job096).
Then classified with Class3D (job100) and select the good particles (job101) to run final refinement (job102).
Final map was generated by Postprocessing (job104) with mask (job103).

Please let me know if you have any questions, thanks.