[Chimera-users] Cut asymmetric unit from volume

Tom Goddard goddard at sonic.net
Fri Jun 3 13:26:19 PDT 2016


Hi Kyle,

  If you have a point symmetry, e.g. icosahedral symmetry, Chimera has no way to extract a wedge of density that is one asymmetric unit.  If you have an atomic model of an asymmetric unit fit into the density, you could extract a box around it using Chimera volume viewer menu entry Features / Atom Box.  Or you could extract the density just at grid points within a specified distance of atoms using volume viewer menu entry Features / Zone….  To save the results of either of those methods use volume viewer menu File / Save Map As….

	Tom


> On Jun 3, 2016, at 11:41 AM, Morris, Kyle wrote:
> 
> Hi Chimera team and users,
> 
> Is there a way to extract the asymmetric unit from a volume which has been 'symmetrised’ from, say for instance, Relion? In this case what are the conventions used by chimera to define the bounds of the sub-volume to extract?
> 
> Thanks for your help!
> 
> Best wishes,
> Kyle
> 
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