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\noindent
Eric Beitz \hfill March 2000

\section*{\TeX{}shade: frequently asked questions }
\bigskip

This is the first release of a FAQ list for \TeX{}shade. Feel free to 
contact me if you have problems, questions or suggestions about the 
package. I will post them and provide hopefully helpful hints in 
future issues of this list.
\bigskip

\noindent
\qquad email: \texttt{eric.beitz@uni-tuebingen.de}
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\noindent
\TeX{}shade: 
\texttt{www.homepages.uni-tuebingen.de/beitz/tse.html}



\subsection*{A. Problems using \TeX{}shade}
\medskip

\begin{enumerate}
    
    \item
    
    \textbf{I cannot \TeX{} the manual because I get the error
    message `\texttt{!\ TeX capacity exceeded, sorry \ldots}'.}
    
    \TeX{}shade needs a lot of memory for setting and shading 
    alignments. The manual is a good test for your memory settings 
    because it uses many alignments and fingerprints, which are 
    in particular memory consuming. If you do not know how to increase 
    \TeX's memory settings, and you do not know a \TeX{} wizard either, then 
    visit the \TeX{}shade homepage at 
    \texttt{http://www.homepages.uni-tuebingen.de/beitz/tse.html} to 
    download the manual in either of three formats: DVI, PDF or 
    PostScript.
    
    
    \item
    
    \textbf{I can set my alignment only when I reduce the number of 
    base-pairs by about 11,000. Otherwise I get the `\texttt{!\ TeX 
    capacity exceeded, sorry \ldots}' error.}
    
    There are several parameters defining \TeX's
    usable space. If you are a \TeX{} wizard (or you know one) 
    increase the values that
    \TeX{}shade complains about during the run in order to set 
    bigger alignments. But do not be disappointed when your \TeX{} 
    system will not set an alignment containing thousands of residues. 
    There is definitely an upper limit (probably the new \LaTeX3 will 
    allow you to use even more memory). Setting alignments is a big job for a 
    typesetting system!
    
    
    \item
    
    \textbf{I want to align 80 sequences but I get the
    `\texttt{!\ No room for a new count}' message.}
    
    For each sequence two counter variables are used by \TeX{}shade, 
    further 14 counters for other purposes are needed (and \TeX{} 
    can handle only 255 counters). This limits the amount of sequences 
    to about 100 in theory. But \LaTeX{} itself and each of 
    the loaded packages allocates more counters further reducing the maximum 
    number of sequences.
    

    \item
    
    \textbf{I receive error messages `\texttt{!\ Missing \$ inserted}' 
    when \TeX ing my alignment. What is wrong?}
    
    At least one of the sequence names in the alignment file contains an
    underscore `\_' symbol. This makes \TeX{} to believe you missed to 
    enter math mode because subscript initiated by an underscore is 
    only allowed in math. You need to change the sequence name(s) either in the 
    alignment file using the `find \& replace' option of your editor or 
    by using the \verb|\nameseq| command in the \TeX shade environment. 
    Nevertheless, subscript and superscript are permitted in sequence names, 
    e.\,g. \verb|\nameseq{1}{Name$_{sub}^{super}$}| will result in 
    Name$_{sub}^{super}$.
    
    
    \item
    
    \textbf{My sequence names start out with a number in the 
    alignment file. Why are they ignored by \TeX{}shade?}
    
    \TeX{}shade analyzes the first character of each line in the 
    alignment file in order to decide whether it is a comment, a 
    ruler or a sequence line etc. All lines starting out with a 
    non-letter character are interpreted as non-sequence lines. Hence, 
    you have to change those names in the alignment file. If you 
    want to have sequence names starting with a number you can  
    use the \verb|\nameseq| command in the \TeX{}shade environment to 
    introduce the number, e.\,g. \verb|\nameseq{1}{57th sequence}|.
    
    
    \item
    
    \textbf{There is an incompatiblity between \TeX{}shade (v1.2)
    and the multi-language package `\texttt{babel}'!}
    
    You are right! The command \verb|\language| is defined in both
    packages which leads to error messages. This bug is fixed since
    the release of \TeX{}shade version 1.3 from March 2000. In this 
    version \verb|\language| is replaced by two commands: 
    \verb|\germanlanguage| and \verb|\englishlanguage|.
    
    
\end{enumerate}



\subsection*{B. Changing the output}
\medskip 

\begin{enumerate}

    \item
    
    \textbf{How can I force \TeX{}shade to print more residues per line?}
    
    Use the \verb|\residuesperline*| command with the `*' extension. 
    This will allow you to set any number of residues per line that is 
    desired, e.\,g. \verb|\residuesperline*{97}|. But then expect numerous 
    `\texttt{!\ Overfull hbox}' errors due to printing lines that 
    are broader than the preset \verb|\textwidth|. The same command 
    without the `*' will calculate the highest number of residues 
    fitting in one line and round it to be divisible by five.

    
    \item
    
    \textbf{Is it possible to add a caption to the \TeX{}shade output?}
    
    Yes, it is. You can embed the \TeX{}shade environment into a 
    `\verb|figure|' with a \verb|\caption|. The only thing you have to 
    keep in mind is, that \TeX{} cannot handle a \verb|figure| 
    environment that is bigger than one page. Thus, as long as your 
    sequence alignment fits on one page and there is still enough 
    space for the caption, it works fine. Otherwise you get 
    `\texttt{!\ Caption out of float}' messages. Nevertheless, in order to 
    add a caption to an alignment that is bigger than one page you have the 
    option to split the alignment into two parts and add the caption 
    to one of them. Further, you could try to append an `empty' figure 
    with a caption to the alignment.
    
    
    \item
    
    \textbf{My alignment file contains the letters `B' and `Z' for 
    Asx and Glx, respectively. How can I apply a special shading for 
    these?}
    
    Use \verb|\funcgroup| to define `B' and `Z' as functional groups 
    and assign the colors and the printing style, e.\,g.
    \medskip
    
    \verb|\funcgroup{B}{White}{Blue}{upper}{up}|
    \smallskip
    
    \verb|\funcgroup{Z}{White}{Red}{upper}{up}|
    \medskip
    
    or add the new residues to an existing group, e.\,g.
    \medskip
    
    \verb|\funcgroup{acidic/amide}{DENQBZ}{Black}{Green}{upper}{up}|.
  
    
    \item

    \textbf{How can I build a legend using the `\texttt{shadebox}' 
    command?}
    
    The \verb|\shadebox| command simply prints a color-filled box at 
    the very location it occurs in the text. This means you have to 
    use \verb|\shadebox| in the normal text rather than inside the 
    \TeX{}shade environment. You find a minimal example below:
    \medskip
    
    \verb|\begin{texshade}{alignmentfile.MSF}|
    \medskip
    
    \qquad \emph{further commands, if needed}
    \medskip
    
    \verb|\end{texshade}|
    \medskip
    
    Legend: 
    
    \qquad\verb|\shadebox{conserved}|: conserved residues 
    
    \qquad\verb|\shadebox{White}|: boring residues
    
    \qquad\verb|\shadebox{Red}|: exciting residues
    
    
\end{enumerate}
    


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