[modeller_usage] Loops

[John Penniston <john AT penniston.com>]

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