I am processing a super-resolution K3 dataset right now. I did the patch motion with 1/2 F crop and got a cleaned particle stack. Now I am planning to try whether local motion can improve the resolution. In the local motion job, it was performed in the raw movies, will the particles coordinate be adjusted since I pick the particles in 2x binned micrograph? And the particles extracted from local motion job, are these un-binned? Thanks
I use the particles and movies from patch motion( I used 1/2 Fcrop in patch motion). I got this figure when I do local motion. Is it normal?
To answer your first question, I believe the binning shouldn’t affect the particle locations – we record particle locations as fractional distance along the micrograph, so it should be independent of shape changes to the micrograph like during F-cropping and binning.
For the second – we have seen a similar issue before (Patch motion correction doesn't show any patch correction) where the trajectories were very jagged, and it appeared that the solution was that the dose parameter was incorrect (the dose-per-frame was input during Import Movies, rather than the total dose across all frames, which is what we expect). Does this perhaps explain the poor trajectories?
Thanks. I do import the total dose(70e/a).
I use the particles from a refinement job and micrograph from the exposure curation job. this is the exposure weight plot
I did a 2d classification after local motion. I can see more junk classes in this job compared to the 2d classification job before local motion. How do I know whether the local motion is doing right?
In general, it’s hard to tell if any of the pre-processing steps (motion correction, CTF estimation, etc.) are improving or hurting results during the 2D classification stage. It might give you a clearer indication about the success if you ran a refinement on the particles before local motion correction, and then an identical refinement using the particles after local motion correction. If the resolution gets worse after local motion that would suggest that something went wrong.