Hi @charliebe2,
Ab-initio reconstruction for helical particles depends significantly on the dataset. For some datasets with helical symmetry that have enough low-resolution features (one example is EMPIAR-10495), ab-initio works excellently because it can use those low-resolution features (that are usually present in globular proteins) to guide search in the early iterations. However, for helical particles with small ASUs (e.g. tobacco mosaic virus), ab-initio exhibits a failure mode that often causes the density to “collapse” from a cylindrical shape to a flattened shape.
We have observed that with some datasets, adjustments to ab-initio’s “Enforce non-negativity” and “Center structures in real space” parameters can improve results. It is worth checking out the suggestions of this thread for more details. Setting the initial and maximum resolution parameters to lower numbers (smaller wavelengths) may also help. But, in our experience, with helical particles the general recommended workflow in these cases is to directly begin with helical refinement, and to generate an initial density via a cylindrical one (this can be done in the “Initial model” section of the helical refinement parameters).
Hope this helps,
Michael