[modeller_usage] Loops

When I attempt to optimize a portion of a molecule for which I don't have a good homolog, the loop optimization procedure always yields a rather nondescript coil with no sheet or helix. Today I tried, as an exercise, to see what "optimization" did to a known crystal structure. I ran the program on the C-terminal helix of calmodulin, a molecule for which the structure is very well known. As has been my experience before, the result was destruction of that nice orderly helix, which was replaced by a coil going off in no particular direction. Can anyone tell me why this happens, and how I can use this procedure to get a better result? Thanks. John Penniston