[Chimera-users] Removing buried substructures

Thomas Goddard goddard at cgl.ucsf.edu
Mon Jul 27 12:25:30 PDT 2009

Hi Brian,

   Segmentation is often difficult and there are a variety of approaches 
  -- which works best depends on the circumstances.  Here are a few ideas.

   If you have molecule models fit into the part of the map you want to 
keep use the color zone tool to color all the density near those 
molecules.  Use the same color for all molecules and the "split map by 
color" button to create two maps, one near the molecules, the other not 
near the molecules.  Even without fit molecules you could place markers 
with the Volume Tracer tool and use those in the same way with split 
map.  A similar effect can be achieved using the volume dialog zone 
panel to restrict map display to a zone around selected molecules or 
markers and then use the volume dialog File / Save Map As... which will 
only save that displayed zone.

   Another approach is to create a surface around the density you want 
to keep or the density you want to remove and then mask using that 
surface with the "mask" Chimera command.  You can hand trace a surface 
with the volume tracer tool drawing loops in several planes and 
connecting the loops to build a surface.  Sometimes you can use a 
gaussian smoothed copy of the map at an appropriate threshold to create 
a masking surface if the region of interest has higher average density. 
  If the region to remove is cylindrical or icosahedral you could use 
the "shape" command to create a standard geometric surface and use it 
for masking.

   With the volume eraser tool it may help to show only a subregion of 
the map so you can see the interior structures you want to erase.  To 
show a subregion you can use the region bounds panel of the volume 
dialog and type in new region bounds, or you can use the subregion 
selection panel and draw an outline box of the subregion and show just 
that region.

   These techniques are described with links to more detailed 
documentation in the Chimera volume guide.


   Chimera segmentation capabilities are limited and this is often the 
hardest part in analyzing EM maps.


-------- Original Message --------
Subject: [Chimera-users] Removing buried substructures
From: Brian & Lanie Grech
To: chimera-users at cgl.ucsf.edu
Date: 7/26/09 7:58 PM

> Hi everyone
> The EM map I am currently working on contains hidden buried 
> substructures and I want to remove these substructures from the map, 
> leaving only the outer layer. Because the map I am working on is very 
> complex, I am finding it difficult to remove the buried substructures 
> using the Volume-eraser Tool. Consequently, I would greatly appreciate 
> any advice on how to remove the buried substructures, without removing 
> the outer layer.
> Thanks
> Brian

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