[Chimera-users] how to mask irregular shape in EM density map

Tom Goddard goddard at sonic.net
Thu Oct 25 16:23:48 PDT 2012

Hi Sy,

   You could trace curves around your object in a few planes to define a 
surface and use that surface to mask the map.  Or you could try a 
watershed segmentation mouse mode.  What works depends on 
characteristics of the actual data.  Videos showing these two techniques 
are on the Chimera web site under video tutorials:





-------- Original Message --------
Subject: [Chimera-users] how to mask irregular shape in EM density map
From: sy31802
To: chimera-users <chimera-users at cgl.ucsf.edu>
Date: 10/24/12 9:12 PM
> Dear all,
> We want to color our EM density map , so we need mask different part 
> of the map in order to distinguish them with different colors. 
> Unfortunately, the sample is not irregular shape , we could not use 
> "shape" to mask volume as usually. Could anyone give some suggestion?
> We also use Amira for 3D rendering. We think the rendering in amira is 
> just the mask, so we want solve the problem the mask the irregular 
> shape with amira , have anyone done with it?
> best regard
> 2012-10-25
> ------------------------------------------------------------------------
> sy31802

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