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+\documentclass[12pt]{article}
+
+
+\begin{document}
+
+
+\noindent
+Eric Beitz \hfill March 2005
+
+\section*{\TeX{}shade: frequently asked questions }
+\bigskip
+
+This is the sixth update of the 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}
+\smallskip
+
+\noindent
+\TeX{}shade:
+\texttt{http://homepages.uni-tuebingen.de/beitz/tse.html}
+
+
+\subsection*{A. Increasing \TeX{}'s memory settings}
+\medskip
+
+ If you are using \TeX{}shade to align several large sequences (about 1000
+ residues/sequence), LaTeX will probably stop compiling and quit with one
+ of the following messages:
+ \texttt{!\ TeX capacity exceeded, sorry [main memory size=384000]} or
+ \texttt{!\ TeX capacity exceeded, sorry [stack size=300]}.
+
+Due to several requests I want to start a list of protocols how
+to increase the standard \TeX{} memory settings for bigger
+alignments. Please contribute to this list by sending me the
+procedure for your particular system.
+
+\begin{enumerate}
+
+ \item
+
+ \textbf{Oz\TeX{} 4.0 for the Macintosh:}
+
+ Find the file `OzTeX:TeX:Configs:Default'. This file contains
+ all memory settings. Look for the section
+ `\% TeX parameters' and increase the values that \TeX{} complains
+ about during the run. You will have to restart Oz\TeX{} before the
+ changes are active.
+
+ For older versions of Oz\TeX{} the configuration file has the
+ same name but the path is somewhat different.
+
+
+ \item
+
+ \textbf{te\TeX{} for *NIX:} (contributed by Joerg Daehn)
+
+ Find the file: `/usr/share/texmf/web2c/texmf.cnf' or
+
+ use \verb|locate texmf.cnf| at the command prompt to find it.
+
+ Login as super user. Backup `texmf.cnf' in case you destroy something and
+ then open the `texmf.cnf' file in your favorite text editor and use its
+ search function to locate \verb|main_memory|. This variable is set to 384000.
+ Change this to some higher value, i.e. 4000000 (works fine for me!). The
+ total amount of memory should not exceed 8000000, so check the other
+ values in that section.
+
+ Next, you want to change the stack size. Search for \verb|stack_size|. This
+ will be set to 300. I changed it to 4000 and it works fine.
+
+ There might be complains by \TeX{} about further specific parameters such
+ as \verb|stack_size|. You find all those in the same file.
+
+ After this you have to run `texconfig init'.
+
+ Logout as root.
+
+ After this all should be set for large alignments. Happy \TeX{}ing!
+
+ The information on how to achieve this was derived from a mail in the
+ te\TeX{} mail archive. The original question was posted by Pascal Francq and
+ answered by Rolf Nieprasch.
+
+
+ \item
+
+ \textbf{MiK\TeX{} for Windows:}
+
+ The MiK\TeX{} documentation describes very detailed how the memory
+ settings can be changed. In brief, you must locate the
+ configuration file `miktex/config/miktex.ini'. In the [MiKTeX]
+ section of this file you find all the parameters you need, e.\,g.\
+ \verb|mem_min|, \verb|mem_max|, \verb|buf_size|, \verb|stack_size| etc.
+
+ It appears, that the standard settings of MiK\TeX{} are bigger
+ than that of other \TeX{} installations, so it may not always be necessary
+ to increase the values.
+
+
+\end{enumerate}
+
+
+\subsection*{B. 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://homepages.uni-tuebingen.de/beitz/tse.html} for
+ downloading 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$_{sub}^{super}$.
+
+ Since v1.3b \TeX{}shade{} is much more tolerant concering special
+ characters. Get it and read the section about sequence names.
+
+
+ \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{Only a fraction of the residues which are supposed to be
+ shaded actually are. Why?}
+
+ Make sure that \TeX{}shade knows when protein sequences are to be
+ set. Align\-ments in the ALN-format do not contain information about the
+ sequence type (DNA or protein). In such cases DNA sequences are
+ assumed by \TeX{}shade leading to a shading of only A's, C's, G's,
+ R's, T's and Y's. A simple solution is to say \verb|\seqtype{P}| in the
+ \verb|texshade| environment.
+
+
+ \item
+
+ \textbf{Functional shading does not work and I get an error message. Why?}
+
+ Same problem as discussed in the point before this one. Functional
+ shading is permitted only on protein sequences. So, tell \TeX{}shade
+ that you are using a protein alignment.
+
+
+ \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|.
+
+ \item
+
+ \textbf{\TeX{}shade crashes when dashes ``-'' are used as gap
+ symbols in alignment input files.}
+
+ Yes. Be careful with all kinds of characters that are ``active''
+ in \TeX{}, such as \verb|$ _ ^ & % " \|. The dash is not really active
+ but two or three consecutive dashes are amalgamated to one longer
+ dash in \TeX. Having those characters in an input file might result
+ in unforeseen errors or even crashes.
+
+ \item
+
+ \textbf{I have problems using PHD predictions in \TeX{}shade. An
+ empty \texttt{.top} or \texttt{.sec} file is created.}
+
+ When you do the PHD run do not restrict the calculation to either
+ secondary structure or topology prediction. Turn on everything.
+ Otherwise the output will have some ambiguous lines which can not
+ be interpreted by \TeX{}shade. Result is an empty
+ \texttt{.top} or \texttt{.sec} file.
+
+\end{enumerate}
+
+
+
+\subsection*{C. 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 `\verb|*|' 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 `\verb|*|' 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. Since \TeX{}shade v1.5 the \verb|\showcaption|
+ command is
+ available to add captions on the top or the bottom of the
+ alignment. The caption behaves exactly as a figure caption
+ including the style, numbering and appearance in the list of
+ figures.
+ \medskip
+
+ Example: \verb|\showcaption{Nice alignment!}|.
+
+
+ \item
+
+ \textbf{I want a short version of the caption for the `List of
+ Figures'. Is this possible?}
+
+ Yes, with \TeX{}shade v1.9 short captions have been introduced.
+ In addition to \verb|showcaption| use the command
+ \verb|shortcaption{|\emph{text}\verb|}|.
+ \medskip
+
+ Example: \verb|\showcaption{Nice alignment!}|\
+ \verb|\shortcaption{Nice}|.
+
+
+ \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 after the \TeX{}shade environment
+ or inside the caption. You find a minimal example below:
+ \medskip
+
+ \qquad\vbox{%
+ \verb|\begin{texshade}{alignmentfile.MSF}|
+ \medskip
+
+ \qquad \verb|\showcpation{Red box: \shadebox{Red}}|
+ \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
+
+
+
+ \item
+
+ \textbf{I do not like the spacing between the feature lines. How
+ can I change it?}
+
+ Employ the respective space controlling command from the
+ following list \verb|\ttopspace|,
+ \verb|\topspace|, \verb|\bottomspace|, \verb|\bbottomspace|.
+ Those are available since \TeX{}shade v1.5 (see manual).
+
+
+
+ \item
+
+ \textbf{How can I change gap and match symbols in diverse mode?}
+
+ Since \TeX{}shade version 1.7, standard definitions for \verb|diverse|
+ mode are:
+
+ \begin{verbatim}
+ \nomatchresidues{Black}{White}{lower}{up}
+ \similarresidues{Black}{White}{lower}{up}
+ \conservedresidues{Black}{White}{{.}}{up}
+ \allmatchresidues{Black}{White}{{.}}{up}
+ \gapchar{-}
+ \end{verbatim}
+
+ After calling \verb|\shadingmode{diverse}| these commands can be
+ used to redefine the \verb|diverse| mode settings (mind the double
+ curly braces around the dot-symbol!).
+
+
+
+ \item
+
+ \textbf{I want to rotate the alignment on the page. Is this possible?}
+
+ Yes. Stefan Vogt has found this solution: use pdflscape.sty and
+ activate it in the preamble with \verb|\usepackage{pdflscape}|. Then
+ put your \TeX{}shade environment inside a \verb|landscape|-environment.
+ You also need to adjust the number of residues per line with
+ \verb|\residuesperline*{number}| to make them fill the rotated page.
+ \medskip
+
+ \qquad\vbox{%
+ \verb|\begin{landscape}|
+
+ \verb|\centering|
+
+ \qquad \verb|\begin{texshade}{alignmentfile.MSF}|
+
+ \qquad \verb|\residuesperline*{|\emph{number}\verb|}|
+ \medskip
+
+ \qquad \qquad \emph{further commands, if needed}
+ \medskip
+
+ \qquad \verb|\end{texshade}|
+
+ \verb|\end{landscape}|
+ }
+
+
+
+ \item
+
+ \textbf{I want use the \TeX{}shade and \TeX{}topo logos in my text. How?}
+
+ Use the commands: \verb|\TeXshade| and \verb|\TeXtopo|.
+
+
+\end{enumerate}
+
+
+
+\end{document} \ No newline at end of file
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