[modeller_usage] homomultimers and symmetry

[Mike White <>]

Hi there,

	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?

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?

Thanks

Mike White