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

[Tom Goddard]

Hi Mike,

  Probably you would just fit a single antibody then replicate it 2 more times to make the C3 symmetry.  You probably don’t need to do the symmetric fitting that takes into account clashes because the antibodies probably do not contact one another.  I can only guess since I know nothing about your data.  For finding the axis for the C3 symmetry I assume your map was computed with C3 symmetry so usually you know the exact axis because you know how the map was computed.  For example if the map is a single spike, then usually the axis would be the z axis.  If you don’t know how it was computed and you have to rederive the axis then you take two copies of the map, rotated one copy by hand approximately 1/3 turn and fit it into the first copy then use the rotation axis reported in the reply log for that fit, or use the "measure rotation” command to find the rotation axis between these two copies of the map.

	Tom


> On Jan 3, 2019, at 10:14 AM, Kent, Michael S wrote:
> 
> Tom,
>  
> Thanks very much for your response.  I have tried to fit a single spike with 3 antibodies that have C3 symmetry but I have not been able to correctly specify the axis vector.  Can you give me some guidance on how to do that?
>  
> Thanks,
>  
> Mike Kent
>  
>  
> From: Tom Goddard 
> Date: Wednesday, January 2, 2019 at 1:31 PM
> To: "Kent, Michael S" 
> Cc: "chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>" <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>>
> Subject: [EXTERNAL] Re: [Chimera-users] fitting antibody and envelope protein structures to EM map of virus: C3 and icosahedral symmetries
>  
> 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.
>  
> Tom
>  
> 
> 
>> 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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