Hi @pozharski! The rationale behind using only a subset of particles for a single-class Ab initio Reconstruction job is explained here.
To summarize you’re essentially right – if you’re requesting only 1 class from Ab initio, that means you think your particle stack is mostly clean. To get the best final map possible, you’ll want to perform Homogeneous Refinement of your particles after Ab initio anyway, so we use a subset to make the Ab initio job faster.