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?