Our CS instance (v 5.0.3) is very insistent in turning off “Recenter with aligned shifts” when extracting particles after a Vol Align Tools job. Even if we turn it on manually, it turns itself off any time we add or remove any micrographs or particles from the inputs (all particles do have aligned shifts).
I think this is not desired behavior based on the documentation I can find, but this isn’t part of my normal workflow, so let me know if it is normal. It is work-aroundable with just toggling it on at the very end before running the job, but it seems a bit odd.
Edited to add: it’s not just when particles are from a Vol Align Tools job, if I connect other particles with align3D (or not) it also turns itself off. Also attached an example here, the “recenter with aligned shifts” is on when I start the job but toggles off when I add any inputs.
Thanks!
Hi @tlevitz ,
This behaviour is intentional when the particle.filament slot is present – this was added to ensure that recentering was, by default, not done with helical particles. This is important for the case where you are applying helical symmetry in Helical Refinement, so that the inter-particle pick distance remains unchanged even when re-extracting. We found that re-centering when doing high-order helical symmetry often caused particles to shift even closer towards one another, which had the effect of losing ASUs in many of particle images. However, these nuances are only really important when helical symmetry is being applied.
A workaround for this is to remove the particle.filament slot from your data. this could be done for example in Volume Alignment Tools job. If you don’t actually need to use Vol Align Tools for its intended purpose at this moment, you could still run particles through the job, remove the filament slot (the x in the upper right corner), and run the job with no recentering (or recenter to N/2, N/2, N/2).
Once the particle.filament slot is gone from your particle stack, all downstream jobs should not invoke this custom logic, so Extract in particular should automatically have re-centering on and not change it. Apologies for the inconvenience here – we’re discussing ways to make this a bit less clunky.
Michael
1 Like
Thanks so much for the explanation – I’m not usually a filament processor, so that makes sense. Should have checked with some non-filament particles before posting!
