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  \gdef\thessect{\subsection{General}}
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\def\ssect#1{
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\includepart{error}
\includepart{warning}
\includepart{note}

\begin{document}
\title{Report of protein analysis}
\author{By the {\sc WHAT IF} program}

\date{2005-03-08%
\footnote{This report was created by WHAT IF version 20030529-0952}}
\maketitle
\section{Introduction}
This document contains a report of findings by the {\sc what if} program
during the analysis of one or more proteins. It contains a separate section
for each of the proteins that have been analysed. Each reported fact has
an assigned severity, one of:
\begin{description}
\item[{\bf error}]: severe errors encountered during the analyses. Items
   marked as errors are considered severe problems requiring immediate
   attention.
\item[{\bf warning}]: Either less severe problems or uncommon structural
   features. These still need special attention.
\item[{\bf note}]: Statistical values, plots, or other verbose results of
   tests and analyses that have been performed.
\end{description}

If alternate conformations are present, only the first is
evaluated.

Hydrogen atoms are only included if explicitly requested, and even then
they are not used by all checks.

\subsection{legend}
Some notations need a little explanation:
\begin{description}
\item[Residue] Residues in tables are normally given in 3--5 parts:
\begin{itemize}
\item A number. This is the internal sequence number of the residue used
      by WHAT IF.
\item The residue name. Normally this is a three letter amino acid name.
\item The sequence number, between brackets. This is the residue number
      as it was given in the input file. It can be followed by the
      insertion code.
\item The chain identifier. A single character. If no chain identifier
      was given in the input file, this will be invisible.
\item A model number (only for NMR structures).
\end{itemize}
\item[Z-Value] To indicate the normality of a score, the score
   may be expressed as a Z-value or Z-score. This is just the number
   of standard deviations that the score deviates from the expected
   value.  A property of Z-values is that the root-mean-square of a
   group of Z-values (the RMS Z-value) is expected to be 1.0. Z-values
   above 4.0 and below $-4.0$ are very uncommon. If a Z-score is used
   in WHAT IF, the accompanying text will explain how the expected
   value and standard deviation were obtained.
\end{description}
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\sect{/u/lytle/bc019267/9valid/c70a/refined\_input/refined\_3.pdb}
\ssect{Symmetry related problems}
\begin{error}
\showsect{Error: Missing unit cell information}
No SCALE matrix is given in the PDB file.
\end{error}

\begin{error}
\showsect{Error: Missing symmetry information}
Problem: No CRYST1 card is given in the PDB file.
\end{error}

