[Chimera-users] tetrahedral symmetry

Tom Goddard goddard at sonic.net
Wed Jun 10 16:23:31 PDT 2015


Hi Kyle,

  Unfortunately Chimera detects tetrahedral symmetry using the EMAN convention and that is not the same orientation as the Xmipp convention.  Specifically EMAN and Xmipp convention have symmetry axis positions differing by an inversion on the z axis.  EMDB 6265 is an example of EMAN convention tetrahedral symmetry that Chimera “measure sym #0” correctly identifies. The “measure sym” command also detects tetrahedral symmetry with 2-fold axes along x,y, and z.

  Of course it would be good if Chimera recognized the Xmipp convention too.  But currently it does not, and does not have a name for the Xmipp convention.

	Tom


> On Jun 9, 2015, at 3:46 PM, Morris, Kyle <Kyle.Morris at warwick.ac.uk> wrote:
> 
> Dear Chimera Developers,
> 
> I have a volume reconstructed from Relion 1.3 imposing tetrahedral symmetry. Curiously, I am not able to find the symmetry group using:
> 
> $ measure symmetry #0
> 
> Chimera returns C3, even with adjusting the parameters it uses to identify the symmetry group. The model is aligned as following the Xmipp convention for T symmetry (http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Symmetry#T) which is the same as what Chimera calls T,z3?
> 
> Any advice on getting the measure command to work in this convention would be greatly appreciated. Thanks!
> 
> Best wishes,
> Kyle Morris
> 
> University of Warwick, UK
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