\section{Script for modeling of loops}
\label{SECTION:loops}

The new loop optimization method relies on a scoring function and optimization 
schedule adapted for loop modeling \cite{FisSal00}. 
The corresponding \TOP\ routine is called
when you set \K{DO\_LOOPS} to \V{1}. Unless you re-define routine
{\tt select\_loop\_atoms}, all regions around gaps in the alignment,
whether they are insertions or deletions, will be optimized thoroughly
after the usual modeling procedure is finished. The loop optimization
relies on a new scoring function adapted for loop modeling.

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\Example{../examples/loop/model-loop.top}
