good to know, I never put it together that it errors when I have many classes but don’t change PCA reconstructions.
I will also swap to Simple and see if I experience a noticeable difference and report back. For the record, I always (and necessarily so) use 0.1 Class Similarity, or else nothing gets separated. Typically 8-10Å Target resolution, this gives a result pretty similar to 3DVA clustering which is principally what I use the tool for; broad classification of motion to isolate ~50k particle clusters where conformation/composition are the same to fast-track my pursuit of high resolution of a subset.