I am still seeing what I assume are artefacts in the components generated by 3D-VA. It doesn’t happen for every dataset, but when it does it manifests as strong lateral banding in the components. In this case, the sample was a membrane protein in a nanodisc (260k particles, junk removed, consensus refinement to 3.3 Å). True heterogeneity is present in some of these modes, I think, but the transitions look a bit messy, I presume due to these artefacts.
I have tried applying a 20Å highpass filter, and increasing lambda all the way up to 0.5, but the artefacts remain in both cases. Suggestions much appreciated!