Thanks mmclean. Let me clarify one thing, I’m doing this through Scipion, so there is a chance that the problem reasides somewhere in metadata conversion. But so far, several attempts have gone great.
Once I have “pruned particles” (though 3 iteration of ab initio (A) or just removing “bad” ctfs (B) I got an initial volume. In A case is already produced since the pruning consist of several ab initio rounds keeping particles of the good volume. In B case have an “ab initio” with 2 classes keeping the “good ones”.
After initial volume, steps are quite straightforward: homogeneous refinement, global ctf refinement, local ctf refinement, final homogeneous refinement.
Since I want to keep both workflow independent, each of the approaches provides their own reference and mask. Mask is a relaxed mask done in both cases with the same parameters. Their reference volume is the best, but I guess is kindoff random.