Hi @olibclarke,
Thanks for the request 
. We have planned investigation of how the refinement jobs handle pseudosymmetric complexes refined in C1, and will look at how well symmetry relaxation helps resolve pseudosymmetry. It would be planned to add this as a feature to homogeneous refinement jobs and local refinement too. Due to the branch-and-bound procedure, there’s a chance that with nearly symmetric complexes refined in C1, particles get misaligned to a symmetry-related position of the correct pose. Thus, with “symmetry relaxation search”, there would be an additional step after branch-and-bound to explicitly check all symmetry-related positions to the found pose (within some deltas around the previously optimal pose), and then use that pose for reconstruction. This is essentially what Daniel Asarnow described in the last paragraph of a previous post – symmetry relaxation without expanded particles.
The second case – making local refinement w/ symmetry relaxation tolerant of symmetry expanded particles – is a bit more complicated. I assume there’s two subcases, both of which I have questions about:
- where all of the N symmetry-related particles from the expanded set are to contribute to the reconstruction after the “symmetry relaxation search”. (Under some constraint that duplicates aren’t superimposed. But is there a reason why the “symmetry relaxation search” is even needed here, since the particles are already expanded and hence already allowed to align independently of each other, centred around each symmetry related pose?)
- where only one symmetry-related particle from the expanded set is to contribute to the reconstruction (the best scoring one, after branch-and-bound alignment. Since particles already cover all of the N symmetry-related poses, no symmetry relaxation search needed. Though, isn’t this just a more computationally expensive version of symmetry relaxation without expanded particles?).
The other complication is due to how particles are processed. Particles are portioned into mini-batches and are aligned via BnB and then immediately accumulated into the reconstruction at their best alignment. If we made this procedure tolerant to symmetry expanded sets, it means that a single mini-batch would have to hold all symmetry-related particles from each of the original particles, so that their alignments or log-probabilities can be compared immediately, in the first and second subcases, respectively. It’s technically possible, but I wonder if there’s a modification of the simpler first case that could result in basically the same behaviour without these complications.
Best,
Michael