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:

    http://www.cgl.ucsf.edu/chimera/videodoc/SurfaceMask

    http://www.cgl.ucsf.edu/chimera/videodoc/segmouse

    http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html

  Tom


-------- Original Message --------
Subject: [Chimera-users] how to mask irregular shape in EM density map
From: sy31802
To: chimera-users <chimera-users@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