[Chimera-users] soft roll off edges with Zone masks

Tom Goddard goddard at sonic.net
Tue Sep 23 16:56:49 PDT 2014


Hi Adam,

  The Chimera “vop falloff” command softens the edges after masking a map.  Here’s a description

	http://www.cgl.ucsf.edu/chimera/data/falloff-sep2012/falloff.html

It basically sets grid values just outside the mask to the average of neighbor values, and repeats that for several iterations to smooth the boundary.  Here is the Chimera documentation.

	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#falloff

  Tom


On Sep 19, 2014, at 4:32 PM, Adam Frost wrote:

> hi Chimera users
> 
> We have determined a pseudo-atomic resolution cryoEM density of a helical co-polymer (two unique chains for the repeating hetero-dimer). We would like to compute map-versus-model FSC curves for each of the unique chains. We'd like to use the Zone tool to mask out the relevant density per chain within ~3A or so of the atoms in our atomic model, but we would like the edges of this mask to be appropriately "soft" (whereas right now zone masking appears to employ a hard edge). has anyone already solved this problem? 
> 
> ~Adam
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