I have generated a protein, and as you can see it seems to have almost a good backbone structure (the helices and the sheets are clearly visible but not quite there). Attached are two photos, Figure 1 is what I have generated, Figure 2 is the original crystal structure.
Is there a way to relax the structure as to emphasise for the secondary structures. In other words, push the structure to form secondary structures? or complete the hydrogen bonds for secondary structures?