Using non-final iteration maps from NU-refinement


Sometimes it appears visually as if the quality of the map form the penultimate or earlier iterations in non-uniform refinement is better than the final map and the FSC profile is nicer. Are there any potential issues with importing this non-final map and using it as a reference in the next refinement job?


No, there’s no issue with it. However, any perceived difference is probably totally irrelevant after the initial low-pass filter before the next refinement.

By final do you mean the sharpened or filtered map? You should always inspect the raw reconstruction map as well. Sometimes, the last iteration could have a bit of overrefinement depending on where the alignment resolution limit was set in the previous iteration. You can try a local refinement with a gentle low-pass, like 6A, and a refinement limit that’s a ~2 A lower than the resolution the FSC curve said you had.