[Chimera-users] fitting antibody and envelope protein structures to EM map of virus: C3 and icosahedral symmetries

Tom Goddard goddard at sonic.net
Wed Jan 2 12:31:49 PST 2019

Hi Mike,

  An icosahedral capsid has twenty 3-fold symmetry axes.  Are the 3-fold symmetric spikes aligned with the 3-fold symmetry axes of the icosahedron?  If they are then imposing the icosahedral symmetry will make the antibody binding to each spike 3-fold symmetric.  If the spike 3-fold symmetry axes are not aligned with the icosahedron 3-fold symmetry axes (seems unlikely) then you would need to know where the spike 3-fold symmetry axes are and in that case I’d suggest fitting an antibody to a single spike using C3 symmetry with an explicitly specified axis vector.


> On Dec 26, 2018, at 4:43 PM, Kent, Michael S wrote:
> I have an EM map for a virus that includes an antibody bound to the envelope proteins.  The envelope proteins are trimers of dimers with C3 symmetry that form spikes on the surface of the virus.   I fit an atomic model for the spikes to the map using icosahedral symmetry, following the very helpful symmetric fitting video tutorial <http://www.cgl.ucsf.edu/chimera/videodoc/SymFitDNAb/>.  Now I am trying to fit a model for the antibody into the spike regions of the map.  I need to impose C3 symmetry for the antibody for the fit into each spike, in addition to imposing icosahedral symmetry to include all the spikes.  How can I impose both of these in the fit?  
> Thanks,
> ​Mike Kent
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