Hi @chenzhao,
Thank you for providing detailed information! This is interesting – just to confirm, are you refining the entire volume, or a significantly smaller portion within the volume? In any case, it is important that the masks used initially have soft edges, and should be generated as described in the “Mask Selection and Generation” section of this case study.
As for the issue of strong ripples in the map as you describe, some users have previously found that in their case, the “ripples” extending over the entire map are only present in the full and sharpened maps – i.e. the A and B half maps don’t have this phenomenon. In the job output, could you download and view either half map in Chimera and let me know if any of them show the “ripples” that you are observing? If the ripples are not present, do the half maps visually show any improvement over the volume that you input into the local refinement job?
This is definitely a bug, and is part of the issues that we hope to resolve in local refinement in future versions; unfortunately though, it is an issue we’ve seen before and don’t have a universal solution to right now. Regardless, do let me know if the half maps from any of your problematic local refinement jobs show this issue too.
I hope this helps, and best regards,
Michael