[Chimera-users] segmentation tool

Tom Goddard goddard at sonic.net
Tue Sep 20 09:45:29 PDT 2011

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.


> 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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> Chimera-users at cgl.ucsf.edu
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