Modellers,

 

            I would like base a homology model for a tetrameric transmembrane protein based on a second homology model of a related protein.

            The template model consists of 4 chains, each with 6 helices.  Loops between several of the helices have been omitted.

            I have used my own alignment and restricted the helical regions using the spatial restraints.

            Because the template contains all 4 chains, I have modelled them together instead of just one.

            However, the model that results is not symmetric across the subunits/chains.

            What is the preferred way to preserve symmetry in a case like this?

 

            Also, because the loops are omitted in the template, I have used chain breaks “/” in the target and gaps “-“ in the template to reproduce the breaks.  That works but then the chain information is lost in the target.

            How can I preserve the chain information?  And can I renumber segments of the target during the modelling procedure?

 

            Thanks,

 

            David