Support for large high symmetry (e.g. viruses) particles in Ab-initio and Hetero-refinement


I have noticed with more than 10 different datasets of virus samples (I symmetry) that both
Ab-initio reconstruction and Heterogeneous Refinement never result in proper 3D densities
when I symmetry is not enforced. Instead, we always get donut/ring-shaped volumes. Enforcing
I symmetry however does result in correct volumes. I am afraid that enforcing symmetry at this
early stage of processing leads to sub-optimal final results. Also, we do try all the tips & tricks
recommended on this board and elsewhere for dealing with symmetries (e.g. increasing batch
size or initial/final resolution etc.), but so far this has not solved our issues in any of our datasets.

I am wondering if there are any plans to introduce new features or optimize workflows for
dealing with high symmetry particles?


I wonder if it’s mostly a sampling issue. If you process these data in Relion, is 7.5 deg. initial sampling sufficient? Also, does homogeneous refinement with some known good particles also fail in C1? If you use the I symmetry classification to throw away junk/non-particles, do these methods continue to fail in C1?

@twg thanks for reporting this.
In addition to the questions from @DanielAsarnow do you notice that if you do ab-initio reconstruction with I-symmetry enforced, and then use that initial model for heterogeneous refinement, do you still end up with donut/ring shaped volumes?