Re: [modeller_usage] homomultimers and symmetry

[Modeller Caretaker <>]

Mike White wrote:
> 	I am new to hands-on experience with Modeller.  I would like to  
> create a homology model of the protein that I am interested in as a  
> homopentamer, using known homopentamer X-ray structures of related  
> proteins. I have run across several questions in the archives about  
> imposing symmetry constraints in the modeling process. Is it  
> necessary to impose such constraints if the template is already a  
> homopentamer with 5-fold symmetry? Doesn't this by itself impose  
> symmetry constraints? Or, is it possible that an energy-minimized  
> structure based on a symmetric template may not retain all of the  
> symmetry of the template and the symmetry restraints make sure that  
> the original symmetry is forced to be retained?

If your template is 5-fold symmetric, it is likely that the model will 
also be 5-fold symmetric, although this of course depends on your 
alignment. Symmetry restraints are more useful if you know something 
about the symmetry of your model, rather than the templates, although 
you can certainly impose whatever restraints you like if the model isn't 
behaving in the way you think it should.

> Finally, since model.symmetry.define() deals with pairs, does one  
> enforce pentameric symmetry in the complex by forcing AB, BC, CD, DE,  
> and EA symmetry, where A-E are the five individual subunits in the  
> homopentamer?

Exactly. There is a sample defsym() routine which does just that at 
http://salilab.org/archives/modeller_usage/2005/msg00142.html

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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