Hey @TMcCorvie,
Right now, local refinement only supports helical symmetry by way of symmetry expansion. It sounds that this could be helpful in your case – after doing the helical refinement, you can read out the final twist, rise, and helical symmetry order parameters from the end of the streamlog, and run a symmetry expansion with those values, and then use those for a future local refinement. You should make sure in the parent helical refinement that the “Limit shifts along the helical axis” is on. The main downside of symmetry expansion is only that it makes your particle stack larger, hence refinements will take longer.
In the specific case of helical symmetry, if you suspect that there’s still flexibility in the central core, you can use a mask that covers fewer asymmetric units. You can do this in the volume tools job – pass in your static mask, and set the “Z-clip fraction (for masks)” parameter to 0.5 for a mask covering 50% of the box size. Also make sure to set all of the other mask parameters (i.e. set the threshold to 1, and use the same dilation radius, padding width, etc. that you used to create the static mask). It’s a tradeoff: with longer masks, flexibility will generate uncertainty around the maximum likelihood alignments, but with shorter masks, you’ll have less signal available for alignment… so more uncertainty again.
There was a recent similar post where I added some other notes about this workflow, but the only catch is that you should make sure that the “Force re-do GS split” parameter is off in the local refinement with expanded particles – this should preserve gold standard independence assumptions.
Best,
Michael