\pagenumbering{roman} 

\vspace{5mm}
\begin{figure}
  \begin{center}
    \includegraphics[scale=1]{figures/scrumps/jpg/polyxmass-logo.jpg}
  \end{center}
  \label{fig:figures/scrumps/psdf/polyxmass-logo}
\end{figure}

\maketitle

\begin{small}
\noindent\textbf{\pxm\ User Manual}\\
Copyright \copyright\ 2001, 2002 by Filippo \textsc{Rusconi}\\

\noindent Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.1 or any later version published by the Free Software Foundation, with no Invariant Sections, with no Front-Cover Texts, and with no Back-Cover Texts. A copy of the license is included in the appendix entitled "GNU Free Documentation License".

The \pxm\ computer program that is described in this document is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. A copy of the license is included in the appendix entitled "GNU General Public License".
     
The \pxm\ computer program that is described in this document is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.\\

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.\\

\noindent For more details see the file \filename{COPYING} in the \pxm\ distribution files.\\
\end{small}

\noindent%
\vspace{5mm}
\textbf{Revision History}
\vspace{-5mm}
\begin{itemize}
\item july 2002, added the section on the molecular calculator (\pxc).
\item july 2002, changed author's address from ``University of Bordeaux'' to ``Present address: Muséum National d'Histoire Naturelle'' in Paris as I have now moved to the Laboratoire de biophysique.
\item july 2002, back to the Computer Modern set of fonts in the text of the manual. pdflatex still best way to get to a nice pdf file.
\item july 2002, added a description of the find/replace procedures.
\item july 2002, made all the big pictures again better managing their size. The overall size of the document has fallen to 2.2 Mb, while it was of more than 5 Mb.
\item april 2002, added a description of how to set some values to customize the program in the resources.tex file. New screen dumps allow to describe the process easily.
\item april 2002, moved general-options.tex to resources.tex.
\item april 2002, changes related to the fact that the packages are no more relocatable.
\item april 2002, changes related to the fact that the directory into which the \pxm\ program is installed is from now on \filename{\pxmr} and not \filename{polyxmass}. So some  macros were edited in order to produce the correct typographical results. The pxm-macros.tex file is not dynamically regenerated from a pxm-macros.tex.in file upon autotools processing. That allows a very close correlation between the version of the software package and the version elements' rendering throughout all the text.
\item april 2002, updated the chapter on the \pxm' filesystem standard to reflect the changes in the program workings (the fact that the ressource files are now in a hidden directory in the user's home directory).
\item april 2002, added a detailed description, in the options' configuration chapter, of each option available.
\item april 2002, added a new chapter on the options' configuration, the file general-options.tex.
\item end of march 2002, added a section on the chemical bridge support.
\item march 2002, moved file names and chapter titles ``config-data.tex'' to ``filesystem-config.tex'' to reflect the real configuration issue that is dealt with in this chapter and to differentiate this configuration issue with the polymer chemistry ``configuration'' or ``definition''.
\item march 2002, added the description of the graphical configuration of the \pxm\ filesystem. Updated relevant parts after the \filename{monomer.dic} file was removed from the configuration files, and its contents are moved to \filename{polymer.dic}.
\item february 2002, added a section on mass searching, as I have coded it these last days.
\item february 2002, chopped polyXmass.tex into chapter parts. This is to allow easily producing chapters one apart from the other.
\item february 2002, added the \fileformat{PDF} thumbnail support with the wonderful package from Heiko Oberdiek (thumbpdf).
\item february 2002, changed the organization of the \pxm-specific chapters into one single chapter, with as many sections as needed to describe all aspects of \pxm' operation;
\item january 2002, added the ``\pxm' Sequence Editor'' chapter;
\item january 2002, added the ``Installing From The \software{rpm} Source Package'' section for the sake of completeness;
\item january 2002, started writing the little (but tough) chapter on the \pxm' configuration data hierarchy scheme;
\item january 2002, a wealth of corrections after careful reading of the last version while in Christmas holidays in Viterbo (near Rome);
\item december 2001, added section on UNIX history\dots\ from document by David A. Wheeler: \emph{Secure Programming for GNU/Linux and UNIX HOWTO};
\item november 2001, switched from DocBook SGML format to \LaTeX format
\item october 2001, initial writing, DocBook SGML format
\end{itemize}

\cleardoublepage
\begin{small}
  \begin{flushright}
    \mbox{}\vspace{30mm}\\
    \textit{To $\mathcal{MARIA\ CECILIA}$,\vspace{5mm}\\
      To all the admirable people acting in the ``\emph{Free Software Movement}'' and in the \textbf{true} ``\emph{Open Source Movement}'' for a better and cleaner computing environment,\vspace{3mm}\\
      To all the readers who helped me with this manual\dots}
  \end{flushright}
\end{small}
\vfill

\cleardoublepage