[Chimera-users] Cut asymmetric unit from volume

Morris, Kyle Kyle.Morris at warwick.ac.uk
Fri Jun 3 15:54:28 PDT 2016


Hi Tom,

Thanks for your response and the info.

Thinking about it, maybe one could create a series of volumes and mask away the density of the symmetric copies so that you’re left with the asymmetric unit?

Kyle

> On 3 Jun 2016, at 13:26, Tom Goddard <goddard at sonic.net> wrote:
> 
> 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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