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

Tom Goddard goddard at sonic.net
Wed Aug 3 18:25:44 PDT 2011

Hi CJ,

   Not sure if you really mean segment, e.g. finding correct molecular 
boundaries, or you just want to make a map that is a wedge with flat 
faces representing the icosahedral asymmetric unit.  If you want the 
latter, here is a video showing how to do it in Chimera using the Color 
Zone split map capability together with marker placement and symmetric 
copies of markers.



> 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.
> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html>
> and commands mask, measure symmetry, segment, vop etc.
> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
> (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:
> <http://plato.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html>
> I hope this helps,
> Elaine
> ----------
> 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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