title: changing TOC font family / removing chapter headings in 'report' document class?

text: I'm new to LaTeX, so please bear with me for a bit if the description of my problem seems incoherent :) I've started to write my thesis using the `report` document class, but I've soon found out that it insists on prepending a redundant `Chapter n` to any chapter I begin. I've tried to work around this by declaring my chapters as `\chapter*{Sneaky chapter}`, but this causes them to be omitted from the TOC. I've switched to the `scrreprt` document class since then, and it does pretty much what I wanted from it regarding the chapter headings, aside from the unsightly sans-serif font it insists on using. So, I've restyled my chapter headings (and sections, and so on and so forth) using the following:               \titleformat{\chapter}       {\normalfont\huge\bfseries}{\thechapter}{1em}{}      Again, this does exactly what it says on the tin, but the headings in the TOC remain in the default sans-serif font. So, in a nutshell, it would be pretty awesome if the chapter headings were set using the default serif font, and the unneeded `Chapter n` gotten rid of. There are no doubt dozens of possible ways to achieve this, I'm sure, but my LaTeX-fu is sadly not up to the task yet.


title: Layout guidelines not exactly a multiple of \baselineskip

text: Many conferences in my area require that papers be submitted on letter paper (8.5" x 11") with 1" margins and a 12pt leading. So we end up with 9" for text. (I'm sure there's a name for that, but it is escaping me.) This gives us 9 in * 72.27 pt/in = 650.43 pt. If we subtract TeX's default `\topskip` = 10 pt for the top line, that gives us 640.43 pt for a little more than 54.3691 lines including the first line. In a one column document, this is typically not an issue since there will be many paragraph breaks between which the extra (approximately) 0.3691 lines can go. In a two column document, this becomes fairly noticeable, especially with long paragraphs. See               \documentclass[twocolumn]{article}     \usepackage{lipsum}     \usepackage[margin=1in]{geometry}     \begin{document}     \lipsum     \lipsum     \end{document}      for an example which isn't terrible, but quite noticeable. One option is to set `\topskip=14.43 pt`. Another option would be to make the bottom margin 76.7 pt. A third option would be to modify both `\topskip` and the bottom margin. A fourth option (which I have used for all of my papers until now) is to just ignore it as it seems highly likely that no one on the program committee will notice and it's certainly not going to make a difference to my acceptance/rejection. Is there a recommended way to handle this?


title: How to draw the diagram of calculating an integral by parts?

text: This diagram (lost a line!) represents the steps to evaluate integral by parts of               $$I = \int{(x^3+3x^2+2x+1)\cdot \mathrm{e}^x \mathrm{d}x}.$$      We have               $$I = (x^3+3x^2+2x+1)\cdot\mathrm{e}^x - (3x^2 + 6x + 2)\cdot\mathrm{e}^x       + (6x+6)\cdot\mathrm{e}^x - 6\cdot\mathrm{e}^x.$$      I don't know how to start. ![enter image description here](http://i.stack.imgur.com/lso3h.jpg) Another integral               $$\int{(x^2+3 x+1)\sin x\,\mathrm{d}x}$$      with diagram ![enter image description here](http://i.stack.imgur.com/8IMHD.jpg) We have               $$-(x^2+3 x+1) \cosx+(2 x+3) \sin  x +2 \cosx. $$      How do the arrows parallel and the signs +, -, +, - (on the arrows) aligned?


title: Is it possible to load a TikZ library locally?

text: Is it possible to load a TikZ library and make it local to a `tikzpicture`? I'm writing a long document, and feel like the different TikZ libraries required for different diagrams are "littering" the namespace.


title: hyperref url breaking

text: References: Forcing linebreaks in \url So, in a plain document with               \usepackage{url}     \begin{document}     You can find this at \url{very-long-url}.     \end{document}      the URL will be broken down, e.g. after slashes. When however `\usepackage{hyperref}` is in effect, breaks are inhibited. I tried adding `\usepackage{breakurl}` below hyperref, and while it does break URLs again, the colorful border that hyperref added is now very faint. How could this last issue be remedied?


title: How to align the equal signs in this equation such that the first line and last 2 lines align

text: so I have an equation below. ![equation image](http://i.stack.imgur.com/AHDBA.jpg) My latex code for it is:               \begin{align*}      CoJPoD_{   \{I_1, \cdots, I_{k-1}, I_{k+1}, \cdots, I_{n}\} | I_{k} }  = CoJPoD_{ \{system \backslash I_{k}\} | I_k}  \\      = P\left( X_1 \ge X_d^{I_1}, \cdots, X_{k-1} \ge X_d^{I_{k-1}}, X_{k+1} \ge X_d^{I_{k+1}}, \cdots, X_n \ge X_d^{I_n} | X_k \ge X_d^{I_k}\right) \\       = \frac{    P\left( X_1 \ge X_d^{I_1}, \cdots, X_{k-1} \ge X_d^{I_{k-1}}, X_k \ge X_d^{I_k}, X_{k+1} \ge X_d^{I_{k+1}}, \cdots, X_n \ge X_d^{I_n}\right)         }{P\left(X_k \ge X_d^{I_k}\right)} \\      = \frac{JPoD_{\{I_1, I_2, \cdots, I_n\}}}{PoD_{I_k}} \\      = \frac{JPoD_{system}}{PoD_{I_k}}     \end{align*}      My question is, how do I make the equal sign in the first line, align with the equal signs in the last 2 lines so that they appear in the "middle" and align the 2 equal signs in line 2 and 3 on the far left. E.g, make it look like this: (I rearranged it in paint lol) ![wanted alignment](http://i.stack.imgur.com/BGnkH.jpg)


title: Bold font error

text: When I type the `ACKNOWLEDGEMENTS` page using bold font, the following text is still bold while it should be normal (not bold). I used this code:               \thispagestyle{fancy}     \rhead{\thepage}  % Sets the right side header to show the page number     \addtolength{\voffset}{0.07in}     \addtolength{\textheight}{1in}     \begin{center}{\normalsize{\bf ACKNOWLEDGEMENTS} \par}\end{center}     {\normalsize     \vspace*{0.35\baselineskip}     \setstretch{0.95}       First, I am grateful to GOD bla bla bla }     \clearpage  % Declaration ended, now start a new page     \cleardoublepage


title: Beamerclass not showing tikz paths as expected

text: I tried the following codesnipped:               \begin{frame}     \begin{tikzpicture}     \tikzstyle{every node} = [draw, align=center,circle, scale = 0.5, thick]     \begin{tabular}{ccc}     \tikz\node (n1) {N1}; &     &      \tikz\node (n2) {N2}; \\     &      \tikz\node (n3) {N3};&      \tikz\node (n4) {N4}; \\     \tikz\node (n5) {N5}; &      \tikz\node (n6) {N6}; &      \tikz\node (n7) {N7};\\     \end{tabular}          \path<1>[blue,->] (n1.south) edge [out= 60, in= 135] (n2.north west);     \path<2>[red,->] (n1.south) edge [out=-70, in=-110] (n3.south);     \end{tikzpicture}     \end{frame}      i does not behave as i expect it to. The paths do not get placed at the nodes but rather somewhere strange. ![enter image description here](http://i.stack.imgur.com/IQJij.gif) How can i fix this and still arrange the notes neatly like they are arranged now?


title: Adding captions and "cont." to framed quotations broken across multiple pages

text: I have to include transcriptions of interviews I had conducted in my thesis, and the institute to which I'll be submitting said thesis is imposing some limitations. The rules are:   * Excerpts should be framed.   * When the text spans multiple pages, each portion should be separately framed.   * Segments of the same dialogue should have the same caption and also the phrase "cont." after each segment, except of course the last. I tried the `mframed` package, but it did not draw the lower/upper boundaries of the frames, so I went with the `framed` package which did the trick. I also chose the `dialogue` environment over `quote` and `quotation`. I still don't know how to   * insert a caption, since this is not a float and making it a float prevents page breaks   * apply the same caption, and hence the same dialogue number to each part   * have LaTeX write "cont." after each part Below is the like to an image of the minimal working example I wrote. I added the "cont." by image editing, to show how it has to look like (without the captions). ![enter image description here](http://i.stack.imgur.com/LjmJu.png) The code used to produce the output above is:               \documentclass[a4paper,onesided,12pt]{report}     \usepackage[utf8x]{inputenc}     \renewcommand{\labelenumi}{(\roman{enumi})}     \usepackage{cite}     \usepackage{framed}     \usepackage{lipsum}     \usepackage{dialogue}     \begin{document}     \lipsum[1-2]     \begin{framed}     \begin{dialogue}         \speak{The Researcher} If you were a teacher, how would you teach physics?         A few seconds of silence         \speak{The Researcher} Have you ever thought, ugh this is boring, I wish it were more like this…         \speak{Student 1} It would probably be more experiment-oriented. I would conduct more experiments.         \speak{Student 2} I would just write on the board like the usual.         \speak{Student 1} Because when it is visual… I would choose to teach using experiments because since experiments are visual they are better able to maintain students’ attention.         \speak{Student 3} I would probably use analogies, you know like with electromagnetic waves. Or mechanics perhaps.  I don’t know which type of wave sound waves are at the present, like those that require a medium or those that do not, I would say something like, I would tell them  for instance to consider sound, is sound mechanical?         \speak{Student 2} Right.         \speak{Student 3} ????? I would get them to remember by doing that, like when they think of sound , it requires a medium for propogation, and thus they would understand the properties of mechanical waves. I would do such things.         \speak{Student 2} I would simply teach by writing on the board, this is the way I learn. I do not like to use visual materials that much.         \speak{Student 4} I would write the summary on the board, and go on that when teaching.         \speak{Student 5} Actually it is good to write…         \speak{Student 2} I would give pointers; which topics produce more questions,  how to solve them…         \speak{Student 5} Our elementary school teacher would give us two weeks to copy a 30-40 page material to paper, since it is easier to remember when you write it. It helped better commit that subject to memory since we also covered the same material in class, but it was boring since you listen to the same things that you wrote down, it was not fun.          \speak{The Researcher} Was copying it to your notebook enough to help you understand it fully that you got bored in class?         \speak{Student 5} You do understand it.         \speak{Student 2} If visual materials, slides or experiments are to be used we have to study daily for us to remember. Yet I forget since I do not study daily.     \end{dialogue}     \end{framed}     \end{document}


title: Why does adding \usepackage{breqn}, even if not used, cause LaTeX compile errors in some places?

text: I have many LaTeX files that includes a common .tex file which has the preamble code. In this include file I added, at the end, this               \usepackage{breqn}      and then run make to build the whole tree. I see now new errors showing in files which compiled ok before. One example was this question Another example is below. The LaTeX code is auto-generated by SWP.               \documentclass[]{article}     \usepackage{amsmath}     \usepackage{amsfonts}     \usepackage{amssymb}     %\usepackage{breqn}  %uncomment this to see the error     \begin{document}     \[     \left(  X\circledast Y\right)  \circledast W={\displaystyle\sum\limits_{l=-\infty}^{\infty}}\left(  \overset{\left(  X\circledast Y\right)  \left(  l\right)}{\overbrace{{\displaystyle\sum\limits_{k=-\infty}^{\infty}}X\left(  k\right)  Y\left(  l-k\right)  }}\right)  W\left(  n-l\right)     \]     \end{document}      ![enter image description here](http://i.stack.imgur.com/MisQB.jpg) uncommenting `\usepackage{breqn}` in the above, gives the error               >pdflatex foo.tex      This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian)      restricted \write18 enabled.          (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)     ! Limit controls must follow a math operator.     <argument> {\displaystyle \sum \limits                                             _{k=-\infty }^{\infty }}X\left ( k\ri...     l.8 ...}X\left(  k\right)  Y\left(  l-k\right)  }}                                                       \right)  W\left(  n-l\right)     ?       I'd like to just understand what is going to help in managing this. I see the error message above, but if the LaTeX code was invalid, then how could it have compiled OK before adding breqn? Why is adding `breqn` causes some compile errors in some places that did not exist before? Using TexLive 2012 debian original package. No changes/addition to it made on my Linux box.


title: list of and add to toc mdframed objects

text: Bellow is some developed example solution I asked here tikz and mdframed + shadow drop and shading               \documentclass{article}     \usepackage[utf8]{inputenc}     \usepackage[T1,T2A]{fontenc}     \usepackage[english,russian]{babel}     \usepackage[a5paper]{geometry}     \usepackage{amsthm,thmtools}     \usepackage[framemethod=tikz]{mdframed}     \usepackage{amsmath,amssymb}     \usetikzlibrary{shadows.blur}     \usetikzlibrary{shapes.symbols}     \usetikzlibrary{shadows,shapes}     \usetikzlibrary{calc}     \usepackage{lipsum}     \newcounter{exercise}     \newtheorem{myexercise}{Exercise}[section]     \tikzset{myshadow/.style={                             % custom shadow with tikz              opacity=.85,              shadow xshift=0.15,              shadow yshift=-0.15,              shade,              shading=axis,              shading angle=230}              }      \tikzstyle{titregris} =     [draw=gray, line width=1.0pt,%              text=white, rectangle,               right,minimum height=.7cm,            double,            shade,                   top color=blue!40,                   bottom color=blue!5,                   rounded corners=8pt,                    opacity=1,                                          shadow xshift=0.15,                                          shadow yshift=-0.15,                                          shade,                                          shading=axis,                                          shading angle=30,                   drop shadow,             ]     \tikzstyle{pointstyle} =     [draw=red, thick, fill=red,%              text=white, rectangle,               right,minimum height=.7cm,            double,            shade,                   top color=red,                   bottom color=blue!5,                   rounded corners=3pt,                   drop shadow             ]                  \renewcommand*\theexercise{Exercise \textnumero\arabic{exercise}}     \makeatletter     \def\mdf@@exercisepoints{}%new mdframed key:     \define@key{mdf}{exercisepoints}{%     \def\mdf@@exercisepoints{#1}     }     \def\mdf@@fig{}%new mdframed key:     \define@key{mdf}{fig}{%     \def\mdf@@fig{#1}     }     \def\mdf@@title{}%new mdframed key:     \define@key{mdf}{title}{%     \def\mdf@@title{#1}     }               \mdfdefinestyle{exercisestyle}{%     middlelinewidth=1.2pt,roundcorner=5pt,linecolor=gray,     %apptotikzsetting={\tikzset{mdfbackground/.append style ={%     %shading = exersicebackground}}},      apptotikzsetting={\tikzset{mdfbackground/.append style={top color=blue!40, bottom color=white}}},     innertopmargin=1.2\baselineskip,     skipabove={\dimexpr0.5\baselineskip+\topskip\relax},     skipbelow={-1em},      shadow=true,      shadowcolor=blue!35,     needspace=3\baselineskip,     frametitlefont=\sffamily\bfseries,     settings={\global\refstepcounter{exercise}},     singleextra={%     \node[titregris,xshift=1cm] at (P-|O) %     {~\mdf@frametitlefont{\theexercise}~\mdf@@title};     \ifdefempty{\mdf@@exercisepoints}%     {}%\node[fill=blue!40,font=\color{black},yshift=-51,circle,inner sep=1pt]     {\node[pointstyle,left,xshift=-1cm] at (P)%     {~\mdf@frametitlefont{\mdf@@exercisepoints pt.}~};},%     \ifdefempty{\mdf@@fig}%     {}%     {\path let \p1=(P), \p2=(O) in node[fill=blue!40,circle,inner sep=1pt,font=\color{white}] at (P|-0,0.5*\y2+0.5*\y1)  {\mdf@@fig};}%      },     firstextra={%     \node[titregris,xshift=1cm] at (P-|O) %     {~\mdf@frametitlefont{\theexercise}~};     \ifdefempty{\mdf@@exercisepoints }%     {}%     {\node[pointstyle,left,xshift=-1cm] at (P)%     {~\mdf@frametitlefont{\mdf@@exercisepoints points}~};},%     {\node[pointstyle, left,xshift=1cm]  {$\clubsuit$};}     },     }     \makeatother     \begin{document}     \begin{mdframed}[style=exercisestyle,exercisepoints=10,fig=$\spadesuit$,title= example $E=mc^2$]     %\begin{myexercise}      \begin{align}                 \dot{n} &= u\cos\psi -v\sin\psi \\                 \dot{e} &= u\sin\psi + v\cos\psi             \end{align}             For small angles the following approximation can be used:             \begin{align}                 \dot{n} &= u -v\delta_\psi \\                 \dot{e} &= u\delta_\psi + v             \end{align}     %\end{myexercise}             \end{mdframed}     \listoftheorems{myexercise}     \end{document}      almost everything can be passed, Now question is can there be "List of Exercise" and "add to toc" commands? Yes thee is a tocloft, but it needs command. With TiKZ this is discussed here Adding TikZ code to TOC . Do i need to wrap mdframed environment with another command? or there can be a another way? p.s. I tryied to use ntheorem to create new theorem , but when i do printing of list theorems it is not pronted in utf-8..It seems conflict with fontencoding..there are broken LIRC commands and i gave up with ntheorem **From here New Qestion starts:** Sorry...I edited and rolled back original code...here is an code developed during discussion. Since that fancy 'suit' node gives problem, when frame splits on tho pages, in coe below i removed it being default. So user can pass 'right side suit fig', when he knows that environment is not splitting. Before if there was no use of this frame splitting was ok...in code below there appeared ne problem: environmet title is lost and only counter value is displayed. here is a code:                   \documentclass{article}     \usepackage[utf8]{inputenc}     \usepackage[T1,T2A]{fontenc}     \usepackage[english,russian]{babel}     \usepackage[a5paper]{geometry}     \usepackage{amsthm,thmtools}     \usepackage[framemethod=tikz]{mdframed}     \usepackage{amsmath,amssymb}     \usetikzlibrary{shadows.blur}     \usetikzlibrary{shapes.symbols}     \usetikzlibrary{shadows,shapes}     \usetikzlibrary{calc}     \usepackage{lipsum}          \newcounter{exercise}          \newtheorem{myexercise}{Exercise}[section]     \tikzset{myshadow/.style={                             % custom shadow with tikz              opacity=.85,              shadow xshift=0.15,              shadow yshift=-0.15,              shade,              shading=axis,              shading angle=230}              }      \tikzstyle{titregris} =     [draw=gray, line width=1.0pt,%              text=white, rectangle,               right,minimum height=.7cm,            double,            shade,                   top color=blue!40,                   bottom color=blue!5,                   rounded corners=8pt,                    opacity=1,                                          shadow xshift=0.15,                                          shadow yshift=-0.15,                                          shade,                                          shading=axis,                                          shading angle=30,                   drop shadow,             ]     \tikzstyle{pointstyle} =     [draw=red, thick, fill=red,%              text=white, rectangle,               right,minimum height=.7cm,            double,            shade,                   top color=red,                   bottom color=blue!5,                   rounded corners=3pt,                   drop shadow             ]                  %\renewcommand*\theexercise{Exercise \textnumero\arabic{exercise}}     \makeatletter     \def\mdf@@exercisepoints{}%new mdframed key:     \define@key{mdf}{exercisepoints}{%     \def\mdf@@exercisepoints{#1}     }     \def\mdf@@fig{}%new mdframed key:     \define@key{mdf}{fig}{%     \def\mdf@@fig{#1}     }     \def\mdf@@title{}%new mdframed key:     \define@key{mdf}{title}{%     \def\mdf@@title{#1}     }               \mdfdefinestyle{exercisestyle}{%     middlelinewidth=1.2pt,roundcorner=5pt,linecolor=gray,      apptotikzsetting={\tikzset{mdfbackground/.append style={top color=blue!40, bottom color=white}}},     innertopmargin=1.2\baselineskip,     skipabove={\dimexpr0.5\baselineskip+\topskip\relax},     skipbelow={-1em},      shadow=true,      shadowcolor=blue!35,     needspace=3\baselineskip,     frametitlefont=\sffamily\bfseries,     singleextra={%     \node[titregris,xshift=1cm] at (P-|O) %     {~\mdf@frametitlefont{Exercise~\textnumero\theexercise}~\mdf@@title};     \ifdefempty{\mdf@@exercisepoints}%     {}%\node[fill=blue!40,font=\color{black},yshift=-51,circle,inner sep=1pt]     {\node[pointstyle,left,xshift=-1cm] at (P)%     {~\mdf@frametitlefont{\mdf@@exercisepoints pt.}~};},%     \ifdefempty{\mdf@@fig}%     {}%     {\path let \p1=(P), \p2=(O) in node[fill=blue!40,circle,inner sep=1pt,font=\color{white}] at (P|-0,0.5*\y2+0.5*\y1)  {\mdf@@fig};}%      },     firstextra={%     \node[titregris,xshift=1cm] at (P-|O) %     {~\mdf@frametitlefont{\theexercise}~};     \ifdefempty{\mdf@@exercisepoints }%     {}%     {\node[pointstyle,left,xshift=-1cm] at (P)%     {~\mdf@frametitlefont{\mdf@@exercisepoints points}~};},%     %{\node[pointstyle, left,xshift=1cm]  {$\clubsuit$};}     },     }     \newcommand\listmdfname{List of Exercises}     \newcommand\listofmdframed{\section*{\listmdfname}%           \@mkboth{\MakeUppercase\listfigurename}%                   {\MakeUppercase\listfigurename}%     \@starttoc{mdf}}     \newenvironment{mythm}[2][]       {\refstepcounter{exercise}\addcontentsline{mdf}{figure}{Exercise~\theexercise~#2}\begin{mdframed}[style=exercisestyle,#1,title=#2]}       {\end{mdframed}}     \makeatother          \begin{document}     \listofmdframed          \begin{mythm}[exercisepoints=10,fig=$\spadesuit$]{Example $E=mc^2$}      \begin{align}                 \dot{n} &= u\cos\psi -v\sin\psi \\                 \dot{e} &= u\sin\psi + v\cos\psi             \end{align}             For small angles the following approximation can be used:             \begin{align}                 \dot{n} &= u -v\delta_\psi \\                 \dot{e} &= u\delta_\psi + v             \end{align}     \end{mythm}          \begin{mythm}[exercisepoints=5,fig=$\spadesuit$]{Example $a=b$}      \begin{align}                 \dot{n} &= u\cos\psi -v\sin\psi \\                 \dot{e} &= u\sin\psi + v\cos\psi             \end{align}             For small angles the following approximation can be used:             \begin{align}                 \dot{n} &= u -v\delta_\psi \\                 \dot{e} &= u\delta_\psi + v             \end{align}     \end{mythm}          \vspace{0.1cm}          Here is problematic example:     \begin{mythm}[exercisepoints=10,]{Example Problematic}      \begin{align}                 \dot{n} &= u\cos\psi -v\sin\psi \\                 \dot{e} &= u\sin\psi + v\cos\psi             \end{align}             For small angles the following approximation can be used:             \begin{align}                 \dot{n} &= u -v\delta_\psi \\                 \dot{e} &= u\delta_\psi + v             \end{align}     \end{mythm}          \begin{mythm}[exercisepoints=5,fig=$\spadesuit$]{Example $a=b$}      \begin{align}                 \dot{n} &= u\cos\psi -v\sin\psi \\                 \dot{e} &= u\sin\psi + v\cos\psi             \end{align}             For small angles the following approximation can be used:             \begin{align}                 \dot{n} &= u -v\delta_\psi \\                 \dot{e} &= u\delta_\psi + v             \end{align}     \end{mythm}     \end{document}      i think passing 'MyTheoremEnv1' as Key instead of having just hardwired text Exercise might solve this?


title: What language is TeX implemented in?

text: I read on Wikipedia that the first version of TeX was written in SAIL. However, does anyone know what language later versions (i.e the current one) are implemented in?


title: ConTeXt problems

text: I am trying to typeset some recipes. I have already tried LaTeX and now I am trying the same/similar with ConTeXt. I am having huge problems with it. I have already been on this for two days and I cannot figure out what is the `context` compiler tell me to do/change/what is the problem. I have tried to figure things out myself. I have read parts of several documents related to ConTeXt: `cont-eni.pdf`, `ms-cb-en.pdf`, `mk.pdf`, `contextref.pdf` Please see my MWE below. Could somebody point out the problems and suggest fixes/better ways to do this?               \setuppapersize[A4]     \setupbodyfont[sansserif,9pt]     \language[cz]          \define[3]\Recipe{%       \section[#1]{#2}%         \startcolumns[n=2,rule=on]           #3         \stopcolumns}          \define[1]\Ingredients{%       \subsubject{Ingredience}%       \it       \starttable[|r|l|]         #1       \stoptable}          \long\def\Steps#1{%       \groupedcommand{\subsubject{Příprava}}{}{#1}}          %\showframe          \starttext     \startalignment[center]       \title{Recepty}       \currentdate     \stopalignment          \chapter{Bábovky}          \Recipe{babovka}{Bábovka}{%       \Ingredients{%         \NC 40~dkg \NC polohrubá mouka \NR         \NC 15~dkg \NC cukr \NR         \NC 10~dkg \NC tuk \NR         \NC 1~ks \NC prášek do pečiva       }       \Steps{%         A word word word word. \par Another word word word word word word         word word word word word word word word word word word word word         word word word word word word word word word word word word word         word word word word word word word word. \par Yet another word         word word word word word word word word word word word word word         word word word word word word word word word word word word word         word word word word word word word word word word word word word         word word word word.\par       }     }          Between. Between. Between. Between. Between. Between. Between.          \Recipe{babovka2}{Bábovka}{%       \Steps{%         Word word word word word word word word word word word word word         word word word word word word word word word word word word word         word word word word word word word word word word word word word.}     }          \page     \completecontent          \stoptext      Compilation log:               (recepty.context.tex          ConTeXt  ver: 2012.05.30 11:26 MKIV  fmt: 2012.10.20  int: english/english          system          > cont-new.mkiv loaded     (/usr/share/texmf/tex/context/base/cont-new.mkiv     system          > beware: some patches loaded from cont-new.mkiv     )     system          > no recepty.context.top     fonts           > latin modern fonts are not preloaded     languages       > language en is active     fonts           > preloading latin modern fonts (third stage)     fonts           > typescripts > unknown: library 'loc'     {/usr/share/texmf/fonts/map/dvips/lm/lm-math.map}{/usr/share/texmf/fonts/map/dvips/lm/lm-rm.map}{/usr/share/texmf/fonts/map/pdftex/context/mkiv-base.map}     fonts           > virtual math > unable to resolve name mapsfromchar     fonts           > fallback modern ss 9pt is loaded     structure       > sectioning > title @ level 2 : 0.0 -> Recepty     backend         > xmp > using file '/usr/share/texmf/tex/context/base/lpdf-pdx.xml'     pages           > flushing realpage 1, userpage 1     structure       > sectioning > chapter @ level 2 : 0.1 -> Bábovky     structure       > sectioning > section @ level 3 : 0.1.1 -> Bábovka     structure       > sectioning > subsubject @ level 4 : 0.1.1.0 -> Ingredience     ! Misplaced \noalign.          system          > tex > error on line 48 in file recepty.context.tex: Misplaced \noalign ...          38       \Steps{%     39         A word word word word. \par Another word word word word word word     40         word word word word word word word word word word word word word     41         word word word word word word word word word word word word word     42         word word word word word word word word. \par Yet another word     43         word word word word word word word word word word word word word     44         word word word word word word word word word word word word word     45         word word word word word word word word word word word word word     46         word word word word.\par     47       }     48 >>  }     49          50     Between. Between. Between. Between. Between. Between. Between.     51          52     \Recipe{babovka2}{Bábovka}{%     53       \Steps{%     54         Word word word word word word word word word word word word word     55         word word word word word word word word word word word word word     56         word word word word word word word word word word word word word.}     57     }     58                    \tablenoalign ->\noalign                               \bgroup \let \noalign \relax \let \tablenoalign \re...     \starttablenoalign ->\tablenoalign                                         \bgroup      \doinserttabletail ->\starttablenoalign                                              \global \settrue \preventtablebreak ...     \stoptable ...hucktableautorow \doinserttabletail                                                        \starttablenoalign \global...     <argument> ...R \NC 1~ks \NC prášek do pečiva }                                                        \Steps {A word word word ...     \Recipe ... [#1]{#2}\startcolumns [n=2,rule=on] #3                                                        \stopcolumns      l.48 }          ?      ! Misplaced \noalign.          system          > tex > error on line 48 in file recepty.context.tex: Misplaced \noalign ...          38       \Steps{%     39         A word word word word. \par Another word word word word word word     40         word word word word word word word word word word word word word     41         word word word word word word word word word word word word word     42         word word word word word word word word. \par Yet another word     43         word word word word word word word word word word word word word     44         word word word word word word word word word word word word word     45         word word word word word word word word word word word word word     46         word word word word.\par     47       }     48 >>  }     49          50     Between. Between. Between. Between. Between. Between. Between.     51          52     \Recipe{babovka2}{Bábovka}{%     53       \Steps{%     54         Word word word word word word word word word word word word word     55         word word word word word word word word word word word word word     56         word word word word word word word word word word word word word.}     57     }     58                    \tablenoalign ->\noalign                               \bgroup \let \noalign \relax \let \tablenoalign \re...     \starttablenoalign ->\tablenoalign                                         \bgroup      \doinserttabletail ...abletail \starttablenoalign                                                        \global \setfalse \prevent...     \stoptable ...hucktableautorow \doinserttabletail                                                        \starttablenoalign \global...     <argument> ...R \NC 1~ks \NC prášek do pečiva }                                                        \Steps {A word word word ...     \Recipe ... [#1]{#2}\startcolumns [n=2,rule=on] #3                                                        \stopcolumns      l.48 }          ?      ! Misplaced \noalign.          system          > tex > error on line 48 in file recepty.context.tex: Misplaced \noalign ...          38       \Steps{%     39         A word word word word. \par Another word word word word word word     40         word word word word word word word word word word word word word     41         word word word word word word word word word word word word word     42         word word word word word word word word. \par Yet another word     43         word word word word word word word word word word word word word     44         word word word word word word word word word word word word word     45         word word word word word word word word word word word word word     46         word word word word.\par     47       }     48 >>  }     49          50     Between. Between. Between. Between. Between. Between. Between.     51          52     \Recipe{babovka2}{Bábovka}{%     53       \Steps{%     54         Word word word word word word word word word word word word word     55         word word word word word word word word word word word word word     56         word word word word word word word word word word word word word.}     57     }     58                    \tablenoalign ->\noalign                               \bgroup \let \noalign \relax \let \tablenoalign \re...     \starttablenoalign ->\tablenoalign                                         \bgroup      \stoptable ...oinserttabletail \starttablenoalign                                                        \globalletempty \dotablehe...     <argument> ...R \NC 1~ks \NC prášek do pečiva }                                                        \Steps {A word word word ...     \Recipe ... [#1]{#2}\startcolumns [n=2,rule=on] #3                                                        \stopcolumns      l.48 }          ?      structure       > sectioning > subsubject @ level 4 : 0.1.1.0 -> Příprava     columns         > balanced in 7 step(s)     structure       > sectioning > section @ level 3 : 0.1.2 -> Bábovka     structure       > sectioning > subsubject @ level 4 : 0.1.2.0 -> Příprava     columns         > balanced in 1 step(s)     pages           > flushing realpage 2, userpage 2     structure       > sectioning > title @ level 2 : 0.1 -> \headtext {content}     pages           > flushing realpage 3, userpage 3      )</usr/share/texmf/fonts/opentype/public/lm/lmsans9-oblique.otf></usr/share/texmf/fonts/opentype/public/lm/lmsans10-regular.otf></usr/share/texmf/fonts/opentype/public/lm/lmsans9-regular.otf>          system          > files > start used files          used files      >    1: filename=recepty.context.tex | foundname=recepty.context.tex | usedmethod=direct     used files      >    2: filename=cont-new.mkiv | filetype=tex | foundname=/usr/share/texmf/tex/context/base/cont-new.mkiv | usedmethod=database     used files      >    3: filename=lang-us.lua | filetype=lua | foundname=/usr/share/texmf/tex/context/patterns/lang-us.lua | usedmethod=database     used files      >    4: filename=lm.lfg | filetype=tex | foundname=/usr/share/texmf/tex/context/fonts/lm.lfg | usedmethod=database     used files      >    5: filename=lm-math.lfg | filetype=tex | foundname=/usr/share/texmf/tex/context/fonts/lm-math.lfg | usedmethod=database     used files      >    6: filename=lm-math.map | filetype=map | format=map | foundname=/usr/share/texmf/fonts/map/dvips/lm/lm-math.map | usedmethod=database     used files      >    7: filename=lm-rm.map | filetype=map | format=map | foundname=/usr/share/texmf/fonts/map/dvips/lm/lm-rm.map | usedmethod=database     used files      >    8: filename=mkiv-base.map | filetype=map | format=map | foundname=/usr/share/texmf/fonts/map/pdftex/context/mkiv-base.map | usedmethod=database     used files      >    9: filename=lmsans9-regular | filetype=otf | format=otf | foundname=/usr/share/texmf/fonts/opentype/public/lm/lmsans9-regular.otf | usedmethod=database     used files      >   10: filename=lmroman5-regular.otf | filetype=otf | format=otf | foundname=/usr/share/texmf/fonts/opentype/public/lm/lmroman5-regular.otf | usedmethod=database     used files      >   11: filename=rm-lmr5.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texmf/fonts/tfm/public/lm/rm-lmr5.tfm | usedmethod=database     used files      >   12: filename=lmmi5.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texmf/fonts/tfm/public/lm/lmmi5.tfm | usedmethod=database     used files      >   13: filename=lmsy5.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texmf/fonts/tfm/public/lm/lmsy5.tfm | usedmethod=database     used files      >   14: filename=lmex10.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texmf/fonts/tfm/public/lm/lmex10.tfm | usedmethod=database     used files      >   15: filename=msam5.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msam5.tfm | usedmethod=database     used files      >   16: filename=msbm5.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm5.tfm | usedmethod=database     used files      >   17: filename=stmary10.afm | filetype=afm | format=afm | foundname=/usr/share/texlive/texmf-dist/fonts/afm/public/stmaryrd/stmary10.afm | usedmethod=database     used files      >   18: filename=stmary10.pfb | filetype=pfb | format=pfb | foundname=/usr/share/texlive/texmf-dist/fonts/type1/public/stmaryrd/stmary10.pfb | usedmethod=database     used files      >   19: filename=lmroman5-bold | filetype=otf | format=otf | foundname=/usr/share/texmf/fonts/opentype/public/lm/lmroman5-bold.otf | usedmethod=database     used files      >   20: filename=lmmib5.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texmf/fonts/tfm/public/lm/lmmib5.tfm | usedmethod=database     used files      >   21: filename=lmsans8-regular.otf | filetype=otf | format=otf | foundname=/usr/share/texmf/fonts/opentype/public/lm/lmsans8-regular.otf | usedmethod=database     used files      >   22: filename=lmmono8-regular.otf | filetype=otf | format=otf | foundname=/usr/share/texmf/fonts/opentype/public/lm/lmmono8-regular.otf | usedmethod=database     used files      >   23: filename=eufm5.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/euler/eufm5.tfm | usedmethod=database     used files      >   24: filename=lmroman7-regular.otf | filetype=otf | format=otf | foundname=/usr/share/texmf/fonts/opentype/public/lm/lmroman7-regular.otf | usedmethod=database     used files      >   25: filename=rm-lmr7.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texmf/fonts/tfm/public/lm/rm-lmr7.tfm | usedmethod=database     used files      >   26: filename=lmmi7.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texmf/fonts/tfm/public/lm/lmmi7.tfm | usedmethod=database     used files      >   27: filename=lmsy7.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texmf/fonts/tfm/public/lm/lmsy7.tfm | usedmethod=database     used files      >   28: filename=msam7.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msam7.tfm | usedmethod=database     used files      >   29: filename=msbm7.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm7.tfm | usedmethod=database     used files      >   30: filename=lmroman7-bold.otf | filetype=otf | format=otf | foundname=/usr/share/texmf/fonts/opentype/public/lm/lmroman7-bold.otf | usedmethod=database     used files      >   31: filename=lmmib7.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texmf/fonts/tfm/public/lm/lmmib7.tfm | usedmethod=database     used files      >   32: filename=eufm7.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/euler/eufm7.tfm | usedmethod=database     used files      >   33: filename=eufb7.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/euler/eufb7.tfm | usedmethod=database     used files      >   34: filename=lmroman9-regular.otf | filetype=otf | format=otf | foundname=/usr/share/texmf/fonts/opentype/public/lm/lmroman9-regular.otf | usedmethod=database     used files      >   35: filename=rm-lmr9.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texmf/fonts/tfm/public/lm/rm-lmr9.tfm | usedmethod=database     used files      >   36: filename=lmmi9.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texmf/fonts/tfm/public/lm/lmmi9.tfm | usedmethod=database     used files      >   37: filename=lmsy9.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texmf/fonts/tfm/public/lm/lmsy9.tfm | usedmethod=database     used files      >   38: filename=msam10.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msam10.tfm | usedmethod=database     used files      >   39: filename=msbm10.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm10.tfm | usedmethod=database     used files      >   40: filename=lmroman9-bold.otf | filetype=otf | format=otf | foundname=/usr/share/texmf/fonts/opentype/public/lm/lmroman9-bold.otf | usedmethod=database     used files      >   41: filename=lmmib10.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texmf/fonts/tfm/public/lm/lmmib10.tfm | usedmethod=database     used files      >   42: filename=lmsans9-regular.otf | filetype=otf | format=otf | foundname=/usr/share/texmf/fonts/opentype/public/lm/lmsans9-regular.otf | usedmethod=database     used files      >   43: filename=lmmono9-regular.otf | filetype=otf | format=otf | foundname=/usr/share/texmf/fonts/opentype/public/lm/lmmono9-regular.otf | usedmethod=database     used files      >   44: filename=eufm10.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/euler/eufm10.tfm | usedmethod=database     used files      >   45: filename=eufb10.tfm | filetype=tfm | format=tfm | foundname=/usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/euler/eufb10.tfm | usedmethod=database     used files      >   46: filename=lang-cs.lua | filetype=lua | foundname=/usr/share/texmf/tex/context/patterns/lang-cs.lua | usedmethod=database     used files      >   47: filename=lmsans10-regular | filetype=otf | format=otf | foundname=/usr/share/texmf/fonts/opentype/public/lm/lmsans10-regular.otf | usedmethod=database     used files      >   48: filename=lpdf-pdx.xml | filetype=tex | foundname=/usr/share/texmf/tex/context/base/lpdf-pdx.xml | usedmethod=database     used files      >   49: filename=lmsans9-oblique | filetype=otf | format=otf | foundname=/usr/share/texmf/fonts/opentype/public/lm/lmsans9-oblique.otf | usedmethod=database          system          > files > stop used files               system          > structure > start used structure          used structure  > text: recepty.context          system          > structure > stop used structure               mkiv lua stats  > used config file          - selfautodir:/share/texmf/web2c/texmfcnf.lua     mkiv lua stats  > used cache path           - readable: '/var/lib/texmf/luatex-cache/context/f919750633122078d706dd10f1cfd39b' (order 1)     mkiv lua stats  > used cache path           - readable: '/home/wilx/.texmf-var/luatex-cache/context/f919750633122078d706dd10f1cfd39b' (order 2)     mkiv lua stats  > used cache path           - writable: '/home/wilx/.texmf-var/luatex-cache/context/f919750633122078d706dd10f1cfd39b'     mkiv lua stats  > resource resolver         - loadtime 0.059 seconds, 3 scans with scantime 0.002 seconds, 20 shared scans, 49 found files, scanned paths: /etc/texmf /home/wilx/.texmf-var /home/wilx/texmf     mkiv lua stats  > stored bytecode data      - 303 modules, 65 tables, 368 chunks     mkiv lua stats  > cleaned up reserved nodes - 39 nodes, 9 lists of 446     mkiv lua stats  > node memory usage         - 3 glue, 2 penalty, 16 attribute, 50 glue_spec, 4 attribute_list     mkiv lua stats  > node list callback tasks  - 6 unique task lists, 5 instances (re)created, 506 calls     mkiv lua stats  > used backend              - pdf (backend for directly generating pdf output)     mkiv lua stats  > loaded patterns           - cs::16 en::2     mkiv lua stats  > jobdata time              - 0.000 seconds saving, 0.000 seconds loading     mkiv lua stats  > callbacks                 - 802 direct, 590 indirect, 1392 total     mkiv lua stats  > lxml preparation time     - 0.000 seconds, 0 nodes, 11 lpath calls, 0 cached calls     mkiv lua stats  > result saved in file      - recepty.context.pdf     mkiv lua stats  > loaded fonts              - 37 files: stmary10.afm eufb10.tfm eufb7.tfm eufm10.tfm eufm5.tfm eufm7.tfm msam10.tfm msam5.tfm msam7.tfm msbm10.tfm msbm5.tfm msbm7.tfm lmmono8-regular.otf lmmono9-regular.otf lmroman5-bold.otf lmroman5-regular.otf lmroman7-bold.otf lmroman7-regular.otf lmroman9-bold.otf lmroman9-regular.otf lmsans10-regular.otf lmsans8-regular.otf lmsans9-oblique.otf lmsans9-regular.otf lmex10.tfm lmmi5.tfm lmmi7.tfm lmmi9.tfm lmmib10.tfm lmmib5.tfm lmmib7.tfm lmsy5.tfm lmsy7.tfm lmsy9.tfm rm-lmr5.tfm rm-lmr7.tfm rm-lmr9.tfm     mkiv lua stats  > fonts load time           - 0.220 seconds      mkiv lua stats  > luatex banner             - this is luatex, version beta-0.70.2-2012091206 (tex live 2012/debian)     mkiv lua stats  > control sequences         - 33699 of 65536 + 100000     mkiv lua stats  > current memory usage      - 52 MB (ctx: 54 MB)     mkiv lua stats  > runtime                   - 2.058 seconds, 2 processed pages, 3 shipped pages, 1.458 pages/second


title: Citing e-books using LaTeX

text: What would be the best way to cite electronic books (e-books) with BibTeX? I am currently using the biblatex-chicago package to produce footnote references. I would like to know what entry type and fields should be used.


title: Maintaining alignment between irregularly vertically spaced TikZ matrix nodes

text: I'm trying to create a diagram with pairs of rectangles of different sizes, each separated by a fixed interval. Additionally, I want each pair to be left- aligned at the same point. Here's an example from my current draft in QTikZ:               \documentclass{memoir}     \usepackage{tikz}     \usetikzlibrary{shapes,snakes}     \usetikzlibrary{positioning}          \begin{document}          \begin{tikzpicture}[scale=2]         \tikzstyle{ann} = [draw=none,fill=none,right]         \matrix[nodes={draw, thick, fill=blue!20,},column 1/.style={anchor=base west},             row sep=0.0cm,column sep=0.5cm]  {         \node[rectangle,fill=green] {Category 1};\\         \node (1) [rectangle] {Lorem ipsum stuff in a wider text box like gibberish, copypasta, limericks, and bathroom graffiti};\\              \node[rectangle,fill=green] {Category 2};\\         \node[rectangle] {Lorem ipsum stuff in a wider text box like gibberish, copypasta, limericks, and bathroom graffiti};\\              \node[rectangle,fill=green] {Content Delivery};\\         \node[rectangle] {This one is much longer -- Lorem ipsum stuff in a wider text box like gibberish, copypasta, limericks, and bathroom graffiti};\\         };     \end{tikzpicture}          \end{document}      ![pic of example without spacing](http://i.stack.imgur.com/Q18pg.png) This one doesn't have the spacing between each pair that I'm looking for, though. Following this question and this question, I tried three different methods for adding that spacing, but always ended up with something like this:               \documentclass{memoir}     \usepackage{tikz}     \usetikzlibrary{shapes,snakes}     \usetikzlibrary{positioning}          \begin{document}              \tikzstyle{ann} = [draw=none,fill=none,right]              \matrix[nodes={draw, thick, fill=blue!20,},column 1/.style={anchor=base west},             row sep=0.0cm,column sep=0.5cm]  {         \node[rectangle,fill=green] {Category 1};\\         \node (1) [rectangle] {Lorem ipsum stuff in a wider text box like gibberish, copypasta, limericks, and bathroom graffiti};\\         };              \begin{scope}[yshift=-1cm]         \matrix[nodes={draw, thick, fill=blue!20,},column 1/.style={anchor=base west},             row sep=0.0cm,column sep=0.5cm]  {         \node[rectangle,fill=green] {Category 2};\\         \node[rectangle] {Lorem ipsum stuff in a wider text box like gibberish, copypasta, limericks, and bathroom graffiti};\\         };         \end{scope}              \begin{scope}[yshift=-2cm]         \matrix[nodes={draw, thick, fill=blue!20,},column 1/.style={anchor=base west},             row sep=0.0cm,column sep=0.5cm]  {         \node[rectangle,fill=green] {Content Delivery};\\         \node[rectangle] {This one is much longer -- Lorem ipsum stuff in a wider text box like gibberish, copypasta, limericks, and bathroom graffiti};\\         };         \end{scope}     \end{tikzpicture}          \end{document}      ![graph with spacing problems](http://i.stack.imgur.com/RCWNQ.png) How do I get the alignments to stay consistent while keeping this heterogeneous spacing?


title: \fullcite of only one member of a set causes the whole set to be cited

text: Consider the following MWE:               \documentclass{article}     \usepackage[ngerman]{babel}     \usepackage[german=quotes                ]{csquotes}     \usepackage[backend=biber,style=chem-angew,subentry=true,                 citetracker=true,maxcitenames=5,mincitenames=4,                 backref=true,backrefsetstyle=setonly,                 ]{biblatex}          \usepackage{filecontents}     \begin{filecontents}{\jobname.bib}     @ARTICLE{tab1,       author = {the Tab1},       title = {Buz},       journal = {J. of Buz},       year = {3001},       volume = {1},       pages = {22}}     @ARTICLE{tab2,       author = {the Tab2},       title = {Buz},       journal = {J. of Buz},       year = {3001},       volume = {1},       pages = {22}}     @SET{tabs,       entryset = {tab1,tab2}}     \end{filecontents}     \addbibresource{\jobname.bib}          \begin{document}     Cite the whole set.\autocite{tabs}     Cite a setmember.\autocite{tab1}     A footnotereference to a set-member cites the whole set.\footfullcite{tab1}     \end{document}      This is what you'll get: ![output of MWE](http://i.stack.imgur.com/QMYXS.jpg) When citing one member of the set, the whole set gets cited. As I understand it the bibliography driver is used to set the `\fullcite`. What I do not understand is how to suppress this behaviour and cite only the given set member. And if this is not possible, at least suppress the unnecessary backreference. Any suggestions?


title: custom text in "list of figures"

text: I am using a template for writing a long document. It automatically creates a list of figures at the start. In the list every entry is nothing but a caption of the figure. In some figures caption string is too long and it doesn't look good. How can I put custom strings in "list of figures"?


title: AUCTeX preview font size too small

text: I have Emacs 24 and AUCTex on a Windows 7 machine, however the preview font size is just way too small. Is there a way to make them bigger? ![enter image description here](http://i.stack.imgur.com/GeNfk.png)


title: Example of a complex compound tikz math statement

text: Could someone provide an example of a complex compound mathematical statement in tikz as I find that most of the answers out there are difficult to understand or lacking. I want a MWE example like this one (note, this one does **not** compile)               \documentclass[landscape]{article}     \usepackage{tikz}     \usepackage{verbatim}     \usepackage[active,tightpage]{preview}     \PreviewEnvironment{tikzpicture}     \setlength\PreviewBorder{5pt}%          \newcommand{\tableXOff}{0.4}     \newcommand{\tableXPad}{\tableXOff}     \newcommand{\tableYOff}{0.1}     \newcommand{\tableYPad}{\tableYOff}     \newcommand{\tableW}{0.5}     \newcommand{\tableH}{0.2}     \newcommand{\xShift}{2}          \usepackage[top=1in,bottom=1in,right=1in,left=1in]{geometry}     \begin{document}     \begin{tikzpicture}[scale=5.3,cap=round,>=latex]        \draw[blue,ultra thick] (-2cm,-2cm) rectangle (2cm,2cm);        \foreach \x in {0,1,...,3} {%           \fill[brown] (\x*(\tableXPad+\tableW)+\tableXOff-\xShift,-\tableYOff) rectangle (\x*0.9+\tableXOff+\tableW-\xShift,-\tableYOff-\tableH);        }        \end{tikzpicture}        \end{document}      So I don't go blind trying to read values, but instead use variables. Unfortunately, the parantheses around `(\tableXPad+\tableW)` cause an error. How do I get around this?


title: Is it possible to use nodes as anchors?

text: I'm trying to recreate a rather complicated reaction scheme with chemfig and TikZ. For that, I'd like to position several amino acid side chains at specific positions. What I'd like to do is to use the "origins" of those side chains as anchors for positioning the molecules: ![MWE](http://i.imgur.com/3av9tUY.jpg) I cannot use normal anchors, however, as the origins' coordinates change depending on the molecules' bounding boxes. Additionally, the chemfig manual states that the origins' coordinates are only calculated when the molecule is actually placed with `\chemfig`. So I thought about using chemfig's `@` syntax to place a node (called `ori`) at the origin and moving the chemfig molecule to it, using the `ori1`/`ori2` nodes as anchors:               \documentclass{article}     \usepackage{chemfig}     \begin{document}       Cysteine side chain            \begin{tikzpicture}         \node[draw,anchor=south west] (cys) at (0,0) {\chemfig{-[@{ori1,0}2]S-H}};         % ??? movement code ???       \end{tikzpicture}            Cysteine side chain, deprotonated            \begin{tikzpicture}         \node[draw, anchor=south west] (cys_deprot) at (0, 0) {\chemfig{-[@{ori2,0}2]S|^{-}}};         % ??? movement code ???       \end{tikzpicture}     \end{document}      However, as far as I've understood from reading through the TikZ manual, there is no way to use other nodes as anchors. Is there some way to achieve this? Edit for clarification: Let's talk about the first structure only, the other one is just for comparision. I'd like to use the bullet in the picture (node `ori1`) as the anchor of the rectangle (node `cys`). However, `ori1`'s coordinates are not known until `cys` is actually placed, which is why I believe I have to do the following dance:   1. Place the `cys` node, so that the `ori1` node gets defined:              \node (cys) at (0,0) {\chemfig{-[@{ori1,0}2]S-H}};        2. Move `cys` to its new (fixed) position, anchored at `ori1`'s coordinates (this is the step I don't know). Is this clear enough? If not, then I'll try and add a picture tonight.


title: Biblatex display format of author name

text: I am looking for a way to make biblatex to display the author names in format of First Middle Initial Last. I want biblatex to automatically convert from other formats of author names to the desired display format. A MWE is like this:               \documentclass[]{article}     \usepackage{filecontents}          \begin{filecontents*}{bib.bib}          @article{jdoe,         author={Doe, John Paul},         journal={Journal},         title={Title},         year=2014,         pages={111--222},     }     \end{filecontents*}          \begin{document}     \noindent Citation: \cite{jdoe}.     \printbibliography[]     \end{document}      I want to know how to add biblatex macros to make the display of the author names to be as John P. Doe, no matter what the format of the author names in .bib are specified. Is there an easy way to do so? I have tried to use `\DeclareNameFormat{first-last}` in the preamble, but this did not work for me. Could you please help? Thanks.


title: Repeat entire table

text: Is there a method to repeat an entire table? I've defined a custom table format using xparse and I have potentially ~50 of these custom tables. I would like to create an appendix of the tables, including all content. I don't want to duplicate the content as it's changing frequently EDIT: One solution is to use a separate file and include it multiple times. This is not a great solution as some of my "tables" are really only 2-3 rows long, and I have a large number of them anyway (e.g. ~50 separate include files would be much harder to work with than the current inline tables)


title: How to clean all personal commands?

text: I'm trying to improve the answers to my other question to create my personal package which provides some commands, like `\alert` to write in red color, or some options like `lineno` to turn on line numbering. But what should I do when I send the `tex` file to someone who don't have the my personal style package? Looking for a solution I tried to check before the document class if my package file exists. If yes, great, load it. But the problem is in negative case. I should to redefine all personal commands or clean all of them to avoid errors. What is the better way to do this?


title: How to arrange floating image top centered?

text: I am using image in my report as follows to make it top centered.                 \documentclass{article}       \usepackage{lipsum}% http://ctan.org/pkg/lipsum       \usepackage{graphicx,caption}% http://ctan.org/pkg/{graphicx,caption}       \begin{document}       \lipsum[1-3]       \begin{figure}[h!]       \includegraphics[width=0.7\linewidth]{example-image-a}       \caption{This is a caption}       \end{figure}       \end{document}      ![enter image description here](http://i.stack.imgur.com/vSLUf.png) But this does not work. If there is one image in page, image is alwasys centered only. How can I make it top centered?


title: ray from the origin of a sphere to the radius

text: In my previous post shifting a sphere, I have two spheres which were lifted from texexamples.net On the left bottom side, there is a sphere with a ray from the center to the radius of the sphere. I can't figure out what the code was for that. I would like to generate a ray on my bigger sphere (left side). I am not sure how though since that code is a little much for me.


title: Removing the line indentation from verses and choruses in a song

text: Friends, consider the following code using the `songs` package:               \documentclass[a4paper]{book}          \usepackage[lyric]{songs}     \usepackage{lipsum}          \renewcommand{\chorusfont}{\bfseries}          \newindex{titleidx}{cbtitle}          \begin{document}          \showindex{My index}{titleidx}          \begin{songs}{titleidx}          \beginsong{My cool song}[       by={John Doe}]          \beginchorus     \lipsum[4]     \endchorus          \beginverse     \lipsum[4]     \endverse          \endsong          \end{songs}          \end{document}      I'm stuck with this line identation from both choruses and verses: ![Songs](http://i.stack.imgur.com/zdEAi.png) I'd like to make the subsequent lines aligned with the first line of the group. I tried to alter the `\versenumwidth` lenght, but it defines the horizontal space reserved for verse numbers to the left. Besides, there is the chorus indentation as well, which I couldn't find anything meaningful. Any ideas?


title: pdf image zoom for Kindle

text: Is it possible to write something into a pdf document so that the Kindle can specifically zoom into an embedded (pdf) image? The Kindle has a 'cursor' and can do that with other (non-pdf) books. I want to do something such as               text tex text text          \pdfsetup{ image={plot_1}, image={     \begin{figure}     \includegraphics{image_name}     \end{figure}}}          text text text text text       with a `\pdfsetup` command similar to hypersetup: Ignored by LaTeX, but put in the pdf document (or something else that works with `\pdfdest`).


title: How to specify default contents for a new .tex file in Emacs?

text: I would like have `Emacs` copy, by default, the contents of some defined file in the buffer of any non-existent `.tex` file I visit. I am using `AUCTeX` and I believe that would be feasible by editing the file or variable that is responsible for appending the lines `%%% Local Variables:`, etc. in new `.tex` files, but I would prefer a solution by way of altering the `.emacs` file, for convenient portability and customizability. In trying to look into it, I did encounter such `Emacs` hooks as `find- file[-noselect]-hook`, but I am unsure of how to specify that a hook will only be run for empty (non-existent) `.tex` files, or which Lisp function copies a file's contents in the current buffer. _Note_ : Use of the `\input{...}` command is not a work-around for what I intend to use this scheme for. To give a small example, I am trying to have the default `.tex` "skeleton" look somewhat like this:               \documentclass[11pt]{article}          \input{$HOME/defaults} %$     \title{ enter title here }          \begin{document}     \maketitle          % document body %          \bibliography{ specify bib file here }          \end{document}      * * * **Update** Thanks to Tom, I've found that I can get the above default contents (and in an actually better way, too) by using `Emacs` skeletons along with `auto-insert- mode`. Hence, I would put the following in my `.emacs` file:               (define-skeleton latex-skeleton       "Default LaTeX file initial contents."       "Title: "       "\\documentclass[11pt]{article}\n\n"       "\\input{\$HOME/defaults} %\$\n"       "\\title{ "str | " ENTER TITLE HERE " "}\n\n"       "\\begin{document}\n"       "\\maketitle\n\n"       ""_"\n\n"       "\\bibliography{" (skeleton-read "BIB-file: ") | " SPECIFY BIB FILE HERE " "}\n\n"       "\\end{document}\n")          (require 'autoinsert)     (add-hook 'find-file-hooks 'auto-insert)     (setq auto-insert-query nil)     (setq auto-insert-alist            '(("\\.tex$" . latex-skeleton)))      However, this does not work for `.tex` files, nor does it work for `latex- mode` (specified by changing the last line above to `'((latex-mode . latex- skeleton)))`)! If, instead, I use any other file extension or `Emacs` major mode it works fine. Therefore, I believe this to be caused by the `AUCTeX`-defined default actions on visiting a new `.tex` file, such as prompting the user to set the master file, appending lines like `%%% Local Variables:`, etc. How could it be possible that I set `AUCTeX` to incorporate my customizations to its defaults? Or would there be some other work-around?


title: texhash: command not found

text: I'm trying to manually install a package on ubuntu, but neither the `sudo texhash` nor the `sudo mktexlsr` command is found by the terminal. `which texhash` returns `/usr/local/texlive/2013/bin/i386-linux/texhash`, so it's there. Do I have to somehow "install" the command?


title: How can I create a decoration that runs down one side of each page?

text: Hi I'm writing an ebook in org-mode that includes a separate .tex file for styles. What I'd like to do is create a box that contains the current chapter and section name on a background image that runs down the left hand side of each page. This side bar should be on each page except the title page, table of contents pages and the first page of a new chapter. At the moment I'm using `memoir` and I'm guessing that this might have something to do with makechapterstyle. However last week was the first time I ever looked at LaTeX so I'm a bit lost! I'd really appreciate some insight into how one would think about solving this with LaTeX, rather than a canned solution - although, obviously I'd appreciate that too :-) On side note - searching for "latex wallpaper" gets some interesting, but not particularly relevant images! **Edit based on Christian's comments** I'm writing a pdf ebook and I'm using the oneside option to memoir. What I want is a thin (1cm or so) image running down the left hand side of every non title page with the name of the section rotated 90˚ overlaid. The title pages will have a slightly wider image and a little bit of blurb. Here's a screenshot of my inspiration: ![Side Projects book](http://i.stack.imgur.com/4UX3b.png)


title: Despite using the 'no markers' option, I still get plotmarks in my legend. Why?

text: Nice to finally post a question myself after finding solutions to my problems on numerous occasions within these forums. I hope someone can be of help (and that this hasn't been asked already). The problem is as follows: I'm using pgfplots for the plots within my document. I used the procedure described in section 4.8.7 (Legends outside of an axis) within the pgfplots manual in order to create one legend for several horizontally aligned plots. In general this works fine. My issue is, that the marker style differs between the plot and the legend. I am using the `no markers` option with `\addplot`. The legend shows the correct line style but also markers. Is it possible to remove the markers? Did I place the `ref{}` command to reference the legend in the wrong place? I couldn't find any solution by browsing google or within the manual, hence my question. The code looks as follows (I can post a minimum working example if necessary):               \begin{figure}[htb]     \centering     \begin{tikzpicture}[baseline]     \begin{axis}     [     legend columns=-1,     legend entries={$Pe_{ax} = 1$;,$Pe_{ax} = 10$;,$Pe_{ax} = 100$;,$Pe_{ax} = 1000$},     legend to name=named3,     width=6cm, height=6cm,      xmin={0},     xmax={2},     ymin={0},     ymax={2},     xtick={0,1,2},     ytick={0,2},     xlabel= {$\Theta [-]$},     ylabel={$E(\Theta) [-]$},     label style={font=\footnotesize},     tick label style={font=\footnotesize},     legend style={draw=none}     ]     \addplot+[no markers,smooth, color=black, dashed] coordinates {(1,0) (1,2)};     \addplot+[no markers,smooth, color=black, dotted] table[x=X,y=Y1] {Tabellen/Butt_1999_Bo1.txt};     \addplot+[no markers,smooth, color=black, dashdotdotted] table[x=X,y=Y1] {Tabellen/Butt_1999_Bo10.txt};     \addplot+[no markers,smooth, color=black, dashdotted] table[x=X,y=Y1] {Tabellen/Butt_1999_Bo100.txt};     \addplot+[no markers,smooth, color=black, solid] table[x=X,y=Y1] {Tabellen/Butt_1999_Bo1000.txt};     \end{axis}     \end{tikzpicture}     \hspace{0cm}     \centering     \begin{tikzpicture}[baseline]     \begin{axis}     [     width=6cm, height=6cm,      xmin={0},     xmax={2},     ymin={0},     ymax={1},     xtick={0,1,2},     ytick={0,1},     xlabel= {$\Theta [-]$},     ylabel={$F(\Theta) [-]$},     label style={font=\footnotesize},     tick label style={font=\footnotesize}     ]     \addplot+[no markers,smooth, color=black, dashed] coordinates {(1,0) (1,1)};     \addplot+[no markers,smooth, color=black, dotted] table[x=X,y=Y2] {Tabellen/Butt_1999_Bo1.txt};     \addplot+[no markers,smooth, color=black, dashdotdotted] table[x=X,y=Y2] {Tabellen/Butt_1999_Bo10.txt};     \addplot+[no markers,smooth, color=black, dashdotted] table[x=X,y=Y2] {Tabellen/Butt_1999_Bo100.txt};     \addplot+[no markers,smooth, color=black, solid] table[x=X,y=Y2] {Tabellen/Butt_1999_Bo1000.txt};     \end{axis}     \end{tikzpicture}     \ref{named3}     \caption{Text.}     \end{figure}      Hope this helps! Thanks in advance for any ideas, thoughts and the like! Edit: as requested here is a minimum working example of the problem.               \documentclass[12pt,a4paper]{article}     \usepackage{pgfplots}     \begin{document}     \begin{figure}[htb]     \centering     \pgfplotsset{domain=-1:1}     \begin{tikzpicture}[baseline]     \begin{axis}     [     legend columns=-1,     legend entries={$x^2$;,$x^3$;,$x^4$;,$x^5$},     legend to name=named,     width=6cm, height=6cm,      xlabel= {$x$},     ylabel={$f(x)$},     legend style={draw=none}     ]     \addplot+[no markers,smooth, color=black, dashed]{x^2};     \addplot+[no markers,smooth, color=black, solid] {x^3};     \addplot+[no markers,smooth, color=black, dashdotdotted] {x^4};     \addplot+[no markers,smooth, color=black, dashdotted] {x^5};     \end{axis}     \end{tikzpicture}     \hspace{0cm}     \centering     \begin{tikzpicture}[baseline]     \begin{axis}     [     width=6cm, height=6cm,      xlabel= {$x$},     ylabel={$f'(x)$},     ]     \addplot+[no markers,smooth, color=black, dashed]{2*x};     \addplot+[no markers,smooth, color=black, solid] {3*x^2};     \addplot+[no markers,smooth, color=black, dashdotdotted] {4*x^3};     \addplot+[no markers,smooth, color=black, dashdotted] {5*x^4};     \end{axis}     \end{tikzpicture}     \ref{named}     \caption{Minimum working example.}     \end{figure}     \end{document}


title: Bioinfo.cls leads to strange ignoring of header

text: ...as you may observe: Here is my LaTeX code:               \documentclass{bioinfo}     \pubyear{2014}     \copyrightyear{2014}     \usepackage{hyperref}     \usepackage{natbib}     \newcolumntype{L}{>{\centering\arraybackslash}m{3cm}}     \usepackage{booktabs, multicol, multirow}     %\usepackage{float}     %\usepackage{round}     \copyrightyear{2014}     \author{Jeffrey Wubbenhorst}     \usepackage{graphicx}          \begin{document}     \firstpage{1}          \title[ ]{Analysis of Prothrombin G20210A in Relation to VTE}%{Visualization}     \author{Jeffrey Wubbenhorst}     \address{ 1219 Broad St, Durham, NC 27705}          \history{Received on May 28th}     \editor{Mr. Robert Gotwals}     %\section{Contact:}\href{Jeffrey Wubbenhorst}{wubbenhorst14j@ncssm.edu}          \maketitle          \iffalse     \documentclass{bioinfo}          \copyrightyear{2014}     \pubyear{2014}     \usepackage{graphicx}          \begin{document}     \firstpage{1}          \title[QTL Analysis]{Evaluation of a QTL Dataset}     \author[Robert R. Gotwals]{Robert R. Gotwals\,\footnote{to whom correspondence should be addressed}}     \address{$^{1}$Department of XXXXXXX, Address XXXX etc.}          \history{Received on XXXXX; revised on XXXXX; accepted on XXXXX}     \editor{Gotwals}     \maketitle     \fi          \begin{abstract}               Computational biology methods were used to visualize the structure and function of prothrombin and thrombin and their interaction with their enzymes and substrates. In addition, exploratory analyses of the theoretical physiologic effects of the prothrombin G20210A mutation in the gene were carried out. These interactions were modeled using the computational methods. This mutation results in abnormally high levels of prothrombin, which in turn lead to higher risks for thrombotic events such as deep vein thrombosis, heart attack, stroke, and pulmonary embolism. Finally, BLAST was used to create a phylogenetic tree of the F2 gene and its variants. clinical outcomes can be improved using thrombin inhibitors and anticoagulants.           \section{Keywords:} \textit{thrombin, G20210A, prothrombin, BLAST, Molegro,  }          \iffalse     \section{Results:}     Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation      \fi               %\section{Contact:} \href{name@bio.com}{name@bio.com}      \end{abstract}          \section{Introduction}     %State clinical relevance!      %Venous thromboembolisms are  is a           \subsection*{Coagulation Cascade}          %This needs to be described in greater detail.      The coagulation system is one of the most important physiologic systems in humans. %Explain importance of coagulation cascade.      The coagulation system balances thrombosis (clotting) thrombolysis (inhibition of clotting) and regulation of platelet function. in order to provide homeostasis and cellular injury, tissue damage and bleeding. %Explain the role of platelets here          The coagulation cascade is one of the most important physiologic systems. It balances thrombosis (clotting), thrombolysis (inhibition of clotting), and regulation of platelet clotting in order to provide homeostasis and protection against cellular damage, tissue damage and bleeding.           The coagulation cascade is a series of processes which lead to the formation of fibrin. (Figure \ref{pathway}) Figure \ref{pathway} is a simplified pathway illustrating the coagulation cascade (image courtesy of Santa Barbara City College).          Fibrin is a protein formed by the interaction between thrombin and fibrinogen. Thrombin, a serine protease, is part of a class of enzymes that cleave peptide bonds in proteins, and is formed from prothrombin by the action of the enzyme prothrombinase (also known as Factor X or thrombokinase). %Add in where proteins are produced, what regulates their production, discuss platelets, where they come from     Prothrombin is a precursor of thrombin, and is encoded by the F2 gene (HGNC ID 3535), located on 11p11.2. Thrombin interacts with at least a dozen substrates, and plays a crucial role in the coagulation cascade. It exists in two forms, inactive and activated.           An accumulation of fibrin results in the formation of blood clots (thrombosis); since fibrinogen is activated by thrombin to produce fibrin, excessive amounts of thrombin (and by extension prothrombin) increase risk for VTE.  \cite{unknown} %I think the cartoon rendering is best, and industry standard     Figure \ref{thrombin} is a rendering of the secondary structure of thrombin, as rendered from PDB ID 2HGT. Figure \ref{prothrombin} is a cartoon rendering of the secondary structure of prothrombin from PDB ID 1PPB.           %\iffalse     \subsection*{Venous Thromboembolism}          A venous thromboembolism (VTE) occurs when a blood clot (or thrombus) forms inside a vein. If thrombus forms within a vein deep in the body, it is called a deep vein thrombosis, or DVT. These are dangerous because they can: (1) increase in size, blocking circulation (2) travel to the lungs, causing a pulmonary embolism, and (3) travel to the brain causing stroke. A wide variety of risk factors are involved in venous thromboembolism, including genetic factors, long-distance travel, and lifestyle. \cite{Hematology} For the purposes of this evaluation, we will be focusing on the influences of G20210A on VTE, which has been associated with major morbidity. Fatal recurrences occur in between 5\% 9\% of patients, causing a significant economic burden to the health care system. \cite{burden, protocol,factors} Clinical trials indicate that heparins can be used to treat some expressions of VTE, though it is not clear if these had any significant influence on mortality. \cite{treatment,PE}     %\fi          \iffalse     \begin{center}     \begin{figure}[ht!]     \centering     \includegraphics[scale=0.25]{fibrinogen.png}     \caption{\textit{Fibrinogen (rendered from PDB 1M1J)}}     \label{fibrinogen}     \end{figure}     \fi                         %I got the image here: http://www.biosbcc.net/doohan/sample/htm/Hemostasis.htm                \subsection*{The Prothrombin G20210A Mutation}     %Discuss blood clots!     %should I talk about how proteins are manufactured?      The prothrombin G20210A mutation in the F2 gene on chromosome 11 is a genetic variant that increases risk for thrombosis. The F2 gene was originally discovered by  Poort, Rosendaal, Reitsma, and Bertina in 1996, and has been well-characterized. \cite{pmid8916933} Along with factor VII, IX, and X, prothrombin is theorized to regulated by molecular mechanisms. \cite{stability} The gene codes for prothrombin (also referred to as coagulation factor II). Prothrombin G20210A (also known as the factor II mutation, or the prothrombin mutation) is a genetic variant of F2, and is the result of a single nucleotide polymorphism, a guanine-adenine switch at F2 position 20210. \cite{sequence} The polymorphism occurs on the noncoding region of the prothrombin gene at position 20210. \cite{pmid8916933} Figure \ref{f2} shows the location of the gene on chromosome 11 (image courtesy of the National Institutes of Health). The G20210A mutation leads to elevated levels of prothrombin, which contributes to hypercoagulability; the latter increases the risk of VTE. Thrombin is also a part of the negative feedback cycle for the coagulation cascade, and abnormal levels thrombin and prothrombin inhibit the normal regulation of blood clotting in multiple ways.      The G20210A mutation occurs primarily in males, and almost exclusively in Caucasians, with roughly 3\% of the population carrying the gene.  \cite{JTH3394, Rosendaal01012005} The mutation has also been associated with obstetric complications and miscarriages. \cite{Obstetric, miscarriage}           %I need to explain what active and inactive forms are! I also need to state how it gets from the inactive to the active states     %Do I need to mention prothrombin time?               \begin{figure}[ht!]     \centering     \includegraphics[scale=0.5,angle=270]{F2.jpg}     \caption{\textit{Cytogenic Location of F2 Gene on Chromosome 11}}     \label{f2}     \end{figure}          %Prothrombin time is a derived measure qunatifying the coagulation time of blood.           \begin{figure}[ht!]     \centering     \includegraphics[scale=0.25]{half_thrombin.png}     \caption{\textit{Thrombin in the Process of Activation}}     \label{half}     \end{figure}          \iffalse     \begin{figure}[ht!]     \centering     \includegraphics[scale=0.15]{Thrombin_Shot.jpg}     \caption{\textit{Active and Inactive Forms of Thrombin}} %What makes these active and inactive?     \label{Active}     %This is a visualization in Molegro of 1MKX.      \end{figure}     \fi                         \subsection*{Molecular Function of G20210A}               The molecular function of the G20210A mutation is not well understood. Kuwahara et al state that           \begin{quotation}     \textit{``Although prothrombin G20210A variant was first found in 1996 as a genetic risk factor of thrombosis, the underlying molecular mechanism for elevation of circulatory prothrombin levels due to the variant has remained elusive."} \cite{MitsuhiroKuwahara11162004}     \end{quotation}          The mechanism by which the G20210A mutation increases thrombotic risk is not well understood. There are three main hypotheses regarding the molecular function of the G20210A mutation:     %Are there really three?          \begin{enumerate}     \item \textit{\textmd{The G20210A mutation leads to higher levels of mRNA expression, leading to higher protein production}}     \item \textit{The G20210A mutation leads to efficiency gains in F2 3' end cleavage signal}  \cite{recognition}     \item \textit{The G20210A mutation increase mRNA instability}     \end{enumerate}          While a consensus has not yet been reached in regards to the method by which G20210A leads to higher prothrombin expression, there is a data supporting the hypothesis that the mutation does not lead to mRNA instability as previously thought.     %I think this may need some more data...                              \begin{methods}     \section{Methods}     % I think I need to reconcile my methods with my computational approach...     %Why is the text formatted differently in the methods section?     \subsection*{Computational Approach}          This investigated used computational biology methods (as noted above) to visualize thrombin structure and function and to model its activity in the coagulation system.      %Finish this later! It is worth noting that this 35% of this grade...               BLAST, the Molegro virtual docker, and the RCSB Protein Data Bank were all utilized to obtain a greater understanding of the coagulation cascade. A comprehensive overview of the F2 gene and the coagulation cascade was accomplished using the RCSB Protein Data Bank, and the NCBI Sequence Viewer.                               \subsection*{Thrombin Pathway}     Pathways for thrombin and warfarin were used to visualize normal coagulation cascade pathways. %Make sure this section is typo-free!           \textit{\textbf{INCLUDE PATHWAYS WITH CAPTIONS}}          \subsection*{BLAST}     % BLAST (Basic Local Alignment Search Tool) was used to identify genetic sequences similar to the healthy F2 sequence. A table with similar sequences is shown below: %This needs to be phrased better.      Analogues to the the F2 gene (NCBI reference sequence NC\_000011.10) were compared using the NCBI BLASTN 2.2.29 algorithm. \cite{algorithm} Compared sequences were then used to create a phylogenetic tree to examine the development of the human prothrombin gene. BLAST data are shown in figure \ref{BLAST}. The phylogenetic tree is shown in figure \ref{Tree}.           \iffalse     \begin{figure}[ht!]     \centering     \includegraphics[scale=0.4, angle=90]{Tree.png}     \caption{\textit{Phylogenetic Tree of BLAST Results}}     \label{Tree}     \end{figure}     \fi               \end{methods}               \section{Results and Discussion}     The G20210A mutation has a significant and unique influence on the proper function of the coagulation cascade, though the mechanism by which it does so is not presently understood.           \subsection*{BLAST}     Results from BLAST are shown in figure \ref{BLAST}.            \vspace{1cm} %I'm adding some space in to keep things from looking cramped.        \begin{figure}[ht!]         \begin{tabular}{|p{3cm}|p{0.75cm}|p{1.25cm}|p{1.75cm}|p{0.75cm}|}%{r|r|r|rr}         \toprule         \textit{\textbf{Description}} & \textit{\textbf{Max Score}} & \textit{\textbf{Total Score}} & \textit{\textbf{Accession}} & \textit{\textbf{Query Cover}} \\         \midrule         Coagulation factor II (thrombin) (F2), RefSeqGene on chromosome 11 & 37515 & 71435 & NG\_008953.1 & 100\% \\         \hline         Chromosome 11, clone RP11-792G9 & 37525 & 1.85E+05 & AC115088.6 & 100\% \\         \hline         Coagulation factor II (thrombin) (F2) gene, complete cds & 37382 & 65528 & AF478696.1 & 100\% \\         \hline         F2 gene, complete cds, Alu and KpnI repeats & 36596 & 68303 & M17262.1 & 100\% \\         \hline         Human gene encoding 5 exons of prothrombin. Exon 1 starts with amino acid position 144 and exon 5 & 8991  & 11357 & V00596.1 & 35\% \\ \hline         Homo sapiens genomic DNA, chromosome 11 clone:RP11-783K16, complete sequence & 761   & 1.28E+05 & AP001453.6 & 31\% \\         \hline         Human DNA sequence from clone RP5-1121G12 on chromosome 20, complete sequence & 756   & 80131 & AL109965.34 & 33\% \\ \hline         Homo sapiens BAC clone RP13-612N21 from 4, complete sequence & 752   & 18352 & AC092458.5 & 22\% \\ \hline         Homo sapiens chromosome 19 clone CTC-483I11, complete sequence & 743   & 1.68E+05 & AC008532.7 & 31\% \\ \hline         Homo sapiens genomic DNA, chromosome 11 clone:RP11-21A7\_A, complete sequence & 743   & 63866 & AP006333.1 & 32\% \\          \bottomrule         \end{tabular}%         \caption{\textit{BLAST Results}}         \label{BLAST}         \end{figure}         \vspace{1cm} %I'm adding some space in to keep things from looking cramped.           BLAST results suggest that there are few documented mutations of the F2 gene. The returned sequences are almost all different versions of the F2 gene, with the exception of  AL109965.34 (a PHD finger protein), chromosome 19 clone CTC-483I11, and clone RP5-1121G12.           \subsection*{Phylogenetic Tree}          Figure \ref{Tree} is a phylogenetic tree as computed using BLAST pairwise alignments. The graphic indicates the similarities between the analyzed genes.           Prothrombin is cleaved by prothrombinase at arg$^{320}$ and arg$^{271}$, which leads to the A-chain and B-chain. The A-chain is non-proteolytic (does not cleave proteins), while the B-chain contains the active sites His57 (histidine-57), Asp102 (aspartic acid 102), and Ser195 (serine 195). The B-chain is known as thrombin. \cite{A_chain} One of thrombin's most important functions is the cleavage of fibrinogen at the N-termini of its A and B chains. This produces a fibrin monomer that can cross-link to itself, producing clot. \cite{pmid10528826, parts,JTH:JTH1363}           \begin{figure}[ht!]     \centering     \includegraphics[scale=0.4, angle=90]{Tree.png}     \caption{\textit{Phylogenetic Tree of BLAST Results}}     \label{Tree}     \end{figure}          \subsection*{Visualization}          The effects of abnormally high levels of thrombin were examined graphically using the Molegro virtual docker. %, which was used to identify points at which ligands      As noted above, the F2 gene codes for prothrombin, which is cleaved at two different sites by activated Factor X (also referred to as Xa or prothrombinase) at arg$^{320}$ and arg$^{271}$. This leads to formation of the A-chain and B-chain. The A-chain is non-proteolytic (does not cleave proteins), while the B-chain contains the active sites His57 (histidine-57), Asp102 (aspartic acid 102), and Ser195 (serine 195).  \cite{A_chain}          %Below is a rendering of the cleavage points of prothrombin:               Figure \ref{1FPH} is a rendering of the interaction between thrombin and fibrinogen. Alpha-chain thrombin is interacting with an analogue of fibrinopeptide A (a substance released when cleaved by fibrinogen) and a C-terminal hirudin peptide (an important factor in the electrostatic interaction with thrombin). \cite{cterminal} It should be noted that the molecules bind to each other in multiple places, which partially accounts for the extreme specificity of thrombin. \cite{specificity} The rendering in figure \ref{half} only involves a segment of fibrinogen.                \subsection*{Molegro Renderings}          Figure \ref{fibrinogen} is an illustration of the secondary structure of fibrinogen (as rendered from PDB ID 1M1J).     Figure \ref{Active} shows inactive thrombin (prothrombin) on the left, and activated thrombin on the right. Figure \ref{half} shows a rendered cartoon of thrombin in the activation process. Figure \ref{1FPH} illustrates the secondary structure of the interaction between thrombin and fibrinogen.                     \begin{center}     \begin{figure}[ht!]     \includegraphics[scale=0.15]{1FPH_(Thrombin+fibrinogen).png}     \caption{\textit{Interaction Between Thrombin Fibrinopeptide A (rendering from PDB 1FPH)}}     \label{1FPH}     \end{figure}     \end{center}          \begin{figure}[ht!]     \centering     \includegraphics[scale=0.25]{fibrinogen.png}     \caption{\textit{Fibrinogen (rendered from PDB 1M1J)}}     \label{fibrinogen}     \end{figure}          The active and inactive forms of thrombin (from left to right) are shown in figure \ref{Active}.           \begin{figure}[ht!]     \centering     \includegraphics[scale=0.15]{Thrombin_Shot.jpg}     \caption{\textit{Active and Inactive Forms of Thrombin}} %What makes these active and inactive?     \label{Active}     %This is a visualization in Molegro of 1MKX.      \end{figure}               \begin{figure}     \centering     \includegraphics[scale=0.25]{Prothrombin.png}     \caption{\textit{Prothrombin (rendered from PDB ID 1PPB)}}     \label{prothrombin}     \end{figure}          \begin{figure}[ht!]     \centering     \includegraphics[scale=0.25]{Thrombin.png}     %     \caption{\textit{Thrombin (rendered from PDB ID 2HGT)}}     \label{thrombin}     \end{figure}          \begin{figure}     \centering     \includegraphics[scale=0.4]{clottingcascade.jpg}     \caption{\textit{Overview of Coagulation Cascade}}     %This image is too shoddy.      \label{pathway}     \end{figure}          \subsection*{Molecular Function of G20210A Mutation}          The exact mechanism of the G20210A mutation is not yet well understood. Ceelie et al state that           \begin{quotation}     \textit{``...it seems less likely that mRNA stability plays a major role in explaining the differences between the levels of the two mRNAs, as there is no difference between the poly(A) tail between 20210A and 20210G mRNA... In conclusion, our data support the idea that the 20210A variation at the 3'-end of the prothrombin gene leads to enhanced 3'-end formation and increased mRNA and protein expression."} \cite[p.~361]{unknown}     \end{quotation}          The poly(A) tail is a chain of adenine nucleotides attached to the end of mRNA that increases mRNA stability. Over time, the tail slowly disintegrates, which leads to the enzymatic breakdown of mRNA. \cite{poly} The fact that the G20210A mutation has no effect on the length of the poly(A) tail is suggestive of another mechanism. A similar view is expressed by Pollack et al, who state that          \begin{quotation}     \textit{``Prothrombin mRNAs that are polyadenylated at position 20210 translate with higher efficiency than mRNAs polyadenylated at position 20212; consequently, 20210A mRNAs (which are all polyadenylated at the translationally active 20210 site) generate more prothrombin than an equal quantity of 20210G mRNAs (most of which are polyadenylated at the translationally quiescent 20212."} \cite{stability}     \end{quotation}          Pollak ete al extend this view slightly:          \begin{quotation}          \textit{``[Evolutionarily related coagulation factor including factors VII,     IX, and X, and protein C.25] factors are encoded by genes     derived from a common prothrombinlike progenitor gene and     possess related functional domains, raising the intriguing possibility     that their expression might be regulated through conserved     molecular mechanisms. "} \cite[p.~126]{stability}     \end{quotation}          \subsection*{Pathways}          Figure \ref{warfarin} shows a pathway for warfarin, a drug commonly used to mitigate symptoms of G20210A (image courtesy of PharmGKB).           \begin{figure}[ht!]     \centering     \includegraphics[scale=0.4, angle=90]{warfarin.png}     \caption{\textit{Warfarin Pathway}}     \label{warfarin}          \end{figure}                    %What is a conserved molecular mechanism?          \section{Conclusions}          Bioinformatics played in integral part in the analysis of the G20210A mutation. Bioinformatics allows us the unique opportunity to observe clinical outcomes as the result of a single polymorphism. This study would not have existed without bioinformatics tools such as BLAST, and Molegro. %This statement will need to be examined again to see if it is appropriate.           \subsection*{Clinical Treatment for Effects of G20210A}          %Here, I will discuss possible treatments for G20210A.      The clinical effects of abnormally high levels of prothrombin due to G20210A can be mitigated in various ways. Anticoagulants (such as coumarin or warfarin) or direct thrombin inhibitors (such as Argatroban or hirudin) have been shown to increase positive outcomes. Emerging developments are being made in the field of new oral anticoagulants, though there is as of yet little information as to their improvement of clinical symptoms. \cite{anti} For VTE in particular, oral anticoagulants are           \section*{Acknowledgments}          Appreciation is extended to Mr. Robert Gotwals for his assistance in this project. This project was funded in part by the NCSSM Foundation. %Is this really something I would like to add in?           \bibliographystyle{unsrtnat} %Find a good way to neaten this up, maybe number my references.      \bibliography{document}                         \end{document}          Thrombin is a serine protease, WHICH IS WHAT?                    Pulmonary embolism has at times been associated with travel (see citation)          The G20210A mutation leads to higher levels of prothrombin, which leads,           I could take a prevention perspective      Illustrated demonstration of mutated thrombin's effects on cascade     I could look at how mutated thrombin increases the risk           from Bob Gotwals to Everyone:     jeffrey do you have a question?     from Jeffrey Wubbenhorst to Everyone:     My study is going well so far, but I'm not entirely certain of the depth to which I should go for this study.     from Jeffrey Wubbenhorst to Everyone:     I'm using Molegro, BLAST, and a few other things here.      from Bob Gotwals to Everyone:     it's a three week project, not a graduate school dissertatin     from Jeffrey Wubbenhorst to Everyone:     Condensed: Do I need to go into any greater detail than I did for a protein profile?     from Bob Gotwals to Everyone:     ok....you have to have some problem or system that you are studying, and ultimately describe how computing helped you understand whatever it is you are doing.     from Jeffrey Wubbenhorst to Everyone:     (Aside from longer iuntroductions and such)     from Jeffrey Wubbenhorst to Everyone:     OK, that really helps. The required length for this paper was 5-6 pages, right?     from Bob Gotwals to Everyone:     well, I won't know until I see it.  It's about a 6 page paper, but I hate giving page limits because you all go absolutely crazy about page counts.  you should create a reasonable document that demonstrates that you know something about the system you are studying, that you used one or more computing tools to study it, and you have some understanding of what your calculations did.               Alpha-thrombin is           1DWB is a crystollographically-obtained analysis of the binding to human thrombin of four active site-directed inhibitors.     F2r=thrombin          polymorphism leads to instability in mRNA     resulting in higher prothrombin           I am examining the clinical results of higher prothrombin levels due to the G20210A mutation using computational biology.                Here is the link (should I need it) of the FASTA for the F2 gene:          http://www.ncbi.nlm.nih.gov/nuccore/NC_000011.10?report=fasta&from=46719192&to=46739506          http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NM_000506          http://omim.org/entry/176930#0009      I am clearly doing something wrong here, as I have an example document that is rendering perfectly. I have about half an hour to get this fixed, or I get a zero on this paper. Any suggestions would be great. EDIT: Just submitted the paper. However, I am very interested in learning the answer to this problem.


title: \href[page=10,pdfremotestartview=FitV] seems not to work

text: I'm trying to get a pdf file I'm composing (using LaTeX et. al.) to have a functional hypertext link that will open a remote pdf file on the web (ideally in the same PDF viewer I'm using to read the one I'm composing although I don't think that's possible is it?) and then navigate to a certain page while fitting the height of that page to the viewing window. Here's my MWE:               \documentclass[12pt]{article}     \usepackage{geometry}      \geometry{letterpaper}       \usepackage{graphicx}     \usepackage{amssymb}     \usepackage[colorlinks=true,urlcolor=cyan]{hyperref}          \title{Brief Article}     \author{The Author}          \begin{document}     \maketitle               I want this \href[page=10,pdfremotestartview=FitV]{http://www.ctex.org/     documents/packages/layout/geometry.pdf}{link} to take me to page 10 of the      linked PDF file while fitting the height of the page to the window. And while      it does switch to my web browser which then downloads the PDF file and opens      that file (using the browser plugin) in a browser window, the browser/plugin      does not navigate to page 10 or fit the vertical height of the page to the      window.          \end{document}      As I write in the MWE, it works part of the way, but not all the way. Am I doing something wrong here? I found this, but I think it's much more complex a problem than the one I face, and although it was helpful to me, it didn't completely solve the problem I'm having now. Any suggestions?


title: Glue at bottom of page

text: I'm writing a lengthy document which will have prompts typically between 2 and 5 lines long with a space after each prompt for notes. Ideally I want a 2-inch space with a stretch of 1 in and a shrink of 0.2 in. The 'internal' prompts are easily handled with `\vspace{2in plus 1in minus 0.2in}`. The problem is at the bottom of the page, since TeX absorbs glue at the bottom of pages. I've tried variations of `\vspace`, `\filbreak`, and `\def\filbreak{\par\vfil\penalty-200\vfilneg}`, adjusting both the `\vfil` and `\vfilneg`. No success. Either the bottom prompt's space is the normal 2 in and the rest are spaced evenly using the remaining space or the bottom space is whatever's left on the page after the others are set to 2 in. Is there any way to (automatically) evenly distribute the spaces?               \documentclass{article}     \usepackage[showframe,margin=1in]{geometry}          %\def\spacer{     %    \par\vspace*{1.7in plus 0.5in minus 0.3in} \penalty-200 %      %    \vfilneg}     \def\comment{The page total is \the\pagetotal. \spacer}     \def\spacer{\par\vspace{2.4in plus 1in minus 0.2in} \penalty-200}     \raggedbottom          \begin{document}           \comment          \comment          \comment          \comment          ...          \comment          \end{document}


title: Glossary as appendix

text: I'm using the `glossaries` package to manage my glossary. This works nicely, except that it forces a page break and creates a huge heading saying Glossary that conflicts with the style of my paper somewhat. Ideally I'd like to stick it in as Appendix A, using the same style for the heading as the Appendix headings, and not messing up the other appendices. Is this possible?


title: Different formatting of footnote mark in text and in footnote

text: I want that my footnotes have numbers like this:   * in the text : like this : `(7)` instead of just `7`.   * in the bottom of the page (where the note text is) : like this : `7\. This is my note... blah...` If I use :                \renewcommand{\thefootnote}{(\arabic{footnote})}      then there is parantheses (...) in the text, but also in the bottom : `(7). This is my note... blah...`, and I don't want this. Any idea?


title: Covered Box Beamer Shadows

text: It seems to me that in beamer, a (rounded) box with shadows that is covered (transparent, normally visible on the next slide) has buggy shadows, I'm not sure if this is a know bug, or maybe an error on my part. My minimal code is the following               \documentclass{beamer}     \usetheme{Warsaw}     \setbeamertemplate{headline}{}     \setbeamertemplate{footline}{}     \setbeamercovered{transparent}     \begin{document}     \begin{frame}     \uncover<2>{     \begin{block}{Head}     Body     \end{block}     }     \end{frame}     \end{document}      ![Result](http://i.stack.imgur.com/OOcO7.png) As you can see, the shadow seems to be above the box. It looks like this both in Acrobat Pro, Reader, and on Ubuntu. Any ideas how I can get rid of it?