Selecting Helical particles after Refinement


I think it would be great if a “particle selection” tool can be added to the “Helical Reconstruction” module. So people can have a chance to get rid of “bad particles” that don’t align so well with the symmetry, or have a large out-of-plane tilt, etc.

For instance, this is the out-of-plane tilt for a correct helical symmetry. This tube has multiple helical symmetries, each different by ~5Å in diameter. So here those particles with >5 degrees tilt particles are quite suspicious and I want to get rid of them. Of course, in other cases, keeping the large tilt particles may not affect the final reconstruction that much. Overall our experience is that getting rid of large out-of-plane tilt particles normally will increase the final resolution a little bit.

Many thanks!

1 Like

Hi @Jerry,

Apologies for the delayed response, and thanks for the feature request :slight_smile: I think there’s a few cases where it would make sense to have a generalized post-refinement particle filtering tool, this definitely being one of them. I’ve made a note of it to consider this down the line.
In the meantime (for anyone interested), subsetting particles based on low-level fields like this is only possible via scripting and modifying the cs files directly. Here, the alignments3D/pose field would have to be converted into euler angles, then subset based on the desired tilt range, written out to a new file, and then finally re-imported back into cryoSPARC via the Import Result Group job. This is definitely tedious and so it would make sense to consider a utility to make this easier.


1 Like