I want to align particles with a ground truth volume generated by atomic model rather than the reconstruct ed map. I wonder how to do only a step of alignment given a map, not the whole refinement job.
BTW, I do not want the map to be lowpassed at the first iteration.
Any advice would help!
Have you read this paper?
Anyway, the alignments are always there, you can use the ones from the first iteration, and set whatever initial low-pass you want, like Nyquist.
I wonder how to use the ones from the first iteration in the “Homogenous Refinement” job?
You can select a specific iteration in the Homogeneous Refinement job’s output tab.