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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