Missing views in 3D reconstruction, how to figure out the wanted 2D classes?

I agree that things don’t look too bad here, but to answer your original question, you could try:

(1) Running the Orientation Diagnostics job. Unfortunately I think there isn’t a way to make it give you more than 12 projections in the “Avg. Relative Signam Amount within Azimuth-Elevation Viewing Regions”, but it does give you a general idea of which projections correspond to which parts of the orientation graph and what the relative signal is, which I find helpful. Plus it gives you the Relion-esque .bild image above this of which directions have more and less signal, which is a little more intuitive for me than just the classic image you show.

(2) You can play around a bit with Create Templates and/or Reference Based Auto Select 2D using “cluster” as the selection mode. The former will give you 2Ds that you can compare to your 2Ds and see if much is missing, and the latter will output a side-by-side of your 2D classes and the 2D classes that may give you something interesting, or may not. It is not formatted for this use (see Allow interactive editing of reference based select 2D? - #7 by olibclarke ; you’re not alone for wanting this), but poking around may give you something.

Edited to add: if your picking is good and your particles are clear in your initial micrographs, it is likely not a picking problem (could be a preferred orientation problem on the grids, or could be some other issue like flexibility etc). I find a lot of users don’t spend enough time looking at their micrographs and their initial picking and then spend a lot of time optimizing picking when in reality those views are just not there. For good micrographs blob picking with some work with the sliders in Inspect Picks does a great job, although Topaz is good for more complex situations, which yours may fall into. If you have everything else great on the micrographs and you think that the preferred orientation is really what is limiting you, try taking a tilted data set and see if the issue resolves.

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