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@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@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

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users