This section describes some of the \MODELLER\ scripts found in the
{\tt \$MODINSTALL6/bin/\_\_*.top} files. All these files and brief 
descriptions are listed in Table~\ref{tab:scripts}.

\begin{table}[hbt]
\begin{center}
\begin{tabular}{ll} \hline
Filename                   & Description \\ \hline
\Scr{model.top}            & the main script for comparative modeling with user alignment\\
\Scr{full\_homol.top}      & the main script for comparative modeling with automatic alignment \\
\Scr{loop.top}             & loop modeling (in development!) \\
\Scr{defs.top}             & variable definitions for modeling by {\tt model} \\
\Scr{align\_strs\_seq.top} & aligning many structures with a sequence\\
\Scr{getnames.top}         & generating default filenames from protein codes \\
\Scr{homcsr.top}           & generating homology-derived restraints \\
\Scr{spline.top}           & generating splined restraints \\
\Scr{cispeptide.top}       & defining {\it cis}-peptides \\
\Scr{default\_patches.top} & making topology patches during modeling by {\tt model}\\
\Scr{special.top}          & generating and reading special restraints/patches for modeling by {\tt model}\\
\Scr{generate\_model.top}  & generating initial models for modeling by {\tt model}\\
\Scr{single\_model.top}    & used by \V{model} to generate a single model \\
\Scr{multiple\_models.top} & used by \V{model} to generate an ensemble of models \\
\Scr{refine.top}           & molecular dynamics refinement for modeling by {\tt model}\\
\Scr{loop.top}             & modeling of loops \\
\Scr{sidehchain.top}       & modeling of a point mutation \\
\Scr{principal.top}        & principal components clustering \\
\Scr{cluster.top}          & optimization by 'clustering' and refinement \\
\Scr{spline. top}          & spline most restraint types in memory \\
\Scr{asgl\_mod.top}        & plotting for clustering analysis (requires \ASGL) \\
\Scr{complete.top}         & generating missing atoms in a PDB file \\
\Scr{fit.top}              & superposing two structures, given an alignment \\
\Scr{mod.top}              & the main include file including all other \Scr{*.top} files \\ \hline
\end{tabular}
\end{center}
\newcommand{\scripts}{{\em List of \MODELLER\ scripts.}}
\caption[\scripts]
{\latex{\scripts}}
\label{tab:scripts}
\underfigtab
\end{table}

\section{Flowchart of comparative modeling by \MODELLER}
\label{SECTION:flowchart}

\input{flowchart.tex} 

% \vspace{1cm}

\section{Script for comparative modeling} \label{model-script}

The \Scr{model} script implements the flowchart for comparative modeling by 
\MODELLER\ that is described in the previous Section~\ref{SECTION:flowchart}. 
The script uses routines in several other files. It is structured
so that it is easy to deal with many different situations, some of which 
are described in Section~\ref{SECTION:faq}. 
The script is too long to be listed here. It can be found in
{\tt \$MODINSTALL6/bin/\-\_\_model.top}. The default values of its
arguments are defined in the \Scr{defs} script file:

{\small
\verbatimfile{../scripts/__defs.top}
}


\input{loops}
