[Chimera-users] Cut asymmetric unit from volume

Tom Goddard goddard at sonic.net
Fri Jun 3 17:02:25 PDT 2016


I don’t understand what this “series of volumes” is you are talking about.  Here’s one idea for defining an asymmetric unit.  Choose a point, apply all the symmetry operators to get N points, and define N asymmetric units one for each of these points consisting of those grid points from the original density map that are closer to that point then the N-1 other points.  You could do this calculation in Chimera with a Python script.

	Tom


> On Jun 3, 2016, at 3:54 PM, Morris, Kyle <Kyle.Morris at warwick.ac.uk> wrote:
> 
> 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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>> 
> 
> 




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