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% This file is a product of WHAT IF. You may use the 
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% program and its authors are appropriately 
% acknowledged. This header is considered to be in
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% Implementation: Rob W.W. Hooft, 1993--1996
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\includepart{error}
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\begin{document}
\title{Report of protein analysis} 
\author{By the {\sc WHAT IF} program}

% Fill in date here
\maketitle
\section{Introduction}
{\sc what\_check}  is the name of the validation option in {\sc what if}. It 
doesn't matter whether you use the {\sc what\_check} program or the
{\sc what if} program for validation. Both produce exactly the same
{\sc what\_check}-report.

This document is a {\sc what\_check}-report that holds the findings of 
the {\sc what if} program
during the analysis of a PDB-file. 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 in all checks. The software functions less well 
for non-canonical amino acids and exotic ligands than for the 20 canonical residues 
and canonical nucleic acids.

\subsection{Some remarks regarding the output:}

\begin{description}
\item[Residue.] Residues/atoms in tables are normally given in a few parts:
\begin{itemize}
\item A number. This is the internal sequence number of the residue used
    by WHAT IF. The first residues in the file get number 1, 2, etc.
\item The residue type. Normally this is a three letter amino acid type.
\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 a minus sign or a blank.
\item A model number. If no model number exists, like in most X-ray files,
    this will be a blank or occasionally a minus sign.
\item In case an atom is part of the output, the atom will be listed using 
    the PDB nomenclature for type and identifier.
\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.
\item[Nucleic acids.] The names of nucleic acids are DGUA, DTHY, OCYT,
   OADE, etc. The first character is a D or O for DNA or RNA respectively.
   This is done to circumvent ambiguities in the many old PDB files in which
   DNA and RNA were both called A, C, G, and T.
\end{description}
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