Hi Jean-François, When you use the Segment Map tool (also known as Segger) and mask the map to a selected region (for example, using menu entry Regions / Mask Map with Selected or File / Save Selected Regions to .mrc File) the new masked map outside the region is set to zero. The segmentation regions only extend to the displayed map contour when used when you created the segmentation. So the rough surface of the masked map is because the map drops to zero abruptly. The only reasonable fix is to use a lower contour level when doing the initial segmentation, a level lower than you will use later when you display masked regions. There is no ability to roll off the mask gradually at the boundary. Tom

Hi,

I am using the segmentation tool on a ~15A cryoEM map. I have noticed that the surface of the mrc maps saved from selected areas look pixelated. Any suggestions how to improve the quality of the segmented maps ?

Best wishes

Jean-François Ménétret

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