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diff --git a/macros/latex/contrib/texshade/tsfaq.tex b/macros/latex/contrib/texshade/tsfaq.tex deleted file mode 100644 index 0ab7a0ec37..0000000000 --- a/macros/latex/contrib/texshade/tsfaq.tex +++ /dev/null @@ -1,432 +0,0 @@ -\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}
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