[Chimera-users] Fwd: [3DEM]asymmetric unit segmentation

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 2 11:24:26 PDT 2011

Hi CJ,
I am hoping somebody with actual experience in this area will respond.

In the meanwhile, however, thought I would mention there are several tools and features in Chimera that may be helpful for editing and segmenting density maps.  You can filter and smooth maps, perform automatic watershed segmentation (but generally after the automatic part you would still need to do things manually -- it is not meant to be completely automatic), create surfaces and mask to those surfaces, color zones to match nearby markers, manually "erase" parts of the map,  etc.

See tools Volume Filter,  Hide Dust, Segment Map, Volume Tracer, Volume Eraser, etc. 

and commands mask, measure symmetry, segment, vop etc.

(measure symmetry is a new feature in 1.6, so you would need the daily build for that)

Guide to volume data display in Chimera:

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 1, 2011, at 12:29 AM, C.J. wrote:

> Dear all,
> I post here for the suggestion of Steven Ludtke in the 3DEM list.
> best regards!
> C.J.
> ---------- Forwarded message ----------
> From: C.J. <biocjh at gmail.com>
> Date: 2011/7/13
> Subject: [3DEM]asymmetric unit segmentation
> To: 3dem at ncmir.ucsd.edu
> Any one have a experience on segmentation of asymmetric unit from
> icosahedron virus structure volume?
> I wonder whether there is any programme could process that automatically?
> Any comment would be appreciated!

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