% 18Mar00 WordForTheWise.tex Damian Counsell % % Word for The Wise: guide to preparing scientific documents with Word % % last modification committed: 28Aug02 % \special{papersize=210mm,297mm} \def\fileversion{2.2} \documentclass[a4paper]{book} \usepackage{graphicx} %comment above line and uncomment line below to convert to pdf %\usepackage[pdftex]{graphicx} \DeclareGraphicsExtensions{.gif,.pdf,.png,.jpg} % also replace all ".eps" with ".jpg" \usepackage{titlesec} \usepackage{titletoc} \usepackage{makeidx} \usepackage{utopia} \usepackage{helvet} \makeindex \begin{document} \titleformat{\chapter}[display] {\fontfamily{bch}\bfseries\LARGE} {\filleft\MakeUppercase{\chaptername} \Huge\thechapter} {4ex} { \vspace{2ex}% \filright} [\vspace{2ex}% ] \titleformat{\section}[hang] {\fontfamily{bch}\bfseries\Large} {\thesection} {8pt} {\Large\bfseries} \titleformat{\subsubsection}[leftmargin] {\normalfont \vspace{6pt}% \sffamily\bfseries\filleft\center} {\thesubsubsection}{.5em}{} \titlespacing{\subsubsection} {4pc}{0.8ex plus .1ex minus .2ex}{1pc} \title{Word for the wise} \author{Damian Counsell} \date{August 2002} \frontmatter \maketitle \section*{This guide is open source}\addcontentsline{toc}{section}{This guide is open source} It is \copyright 1998-2002 by Damian Counsell, email: word@counsell.com\\ For the latest version of this book go to: \begin{quote} http://www.counsell.com/wordforthewise/ \end{quote} You can print it out, read and use it in any way you want provided you meet the conditions of the Open Publication Licence under which it is released---and those terms include the options I have specified (see below). This material may be distributed only subject to the terms and conditions set forth in the Open Publication License, v1.0 or later (the latest version of this licence is presently available at: \begin{quote} http://www.opencontent.org/openpub/ \end{quote} .) \section*{Open Publication Licence}\addcontentsline{toc}{section}{Open Publication Licence} This book is an Open Publication, released under the Open Publication Licence. Below I include Draft v1.0 of that licence, dated, 8 June 1999. \subsection*{I\@. Requirements on both unmodified and modified versions} The Open Publication works may be reproduced and distributed in whole or in part, in any medium physical or electronic, provided that the terms of this license are adhered to, and that this license or an incorporation of it by reference (with any options elected by the author(s) and/or publisher) is displayed in the reproduction. \paragraph*{Proper form for an incorporation by reference is as follows:} \begin{quote} Copyright (\copyright) $<$year$>$ by $<$author's name or designee$>$. This material may be distributed only subject to the terms and conditions set forth in the Open Publication License, vX.Y or later (the latest version is presently available at: \begin{quote} \texttt{http://www.opencontent.org/openpub/} \end{quote} \end{quote} The reference must be immediately followed with any options elected by the author(s) and/or publisher of the document (see section VI). Commercial redistribution of this Open Publication-licensed material is only permitted according to the conditions set out in section VI. Any publication in standard (paper) book form shall require the citation of the original publisher and author. The publisher and author's names shall appear on all outer surfaces of the book. On all outer surfaces of the book the original publisher's name shall be as large as the title of the work and cited as possessive with respect to the title. \subsection*{II\@. COPYRIGHT} The copyright to each Open Publication is owned by its author(s) or designee. \subsection*{III\@. SCOPE OF LICENCE} The following licence terms apply to all Open Publication works, unless otherwise explicitly stated in the document. Mere aggregation of Open Publication works or a portion of an Open Publication work with other works or programs on the same media shall not cause this licence to apply to those other works. The aggregate work shall contain a notice specifying the inclusion of the Open Publication material and appropriate copyright notice. \paragraph{Severability:} If any part of this license is found to be unenforceable in any jurisdiction, the remaining portions of the license remain in force. \paragraph{No warranty:} Open Publication works are licensed and provided ``as is'' without warranty of any kind, express or implied, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose or a warranty of non-infringement. \subsection*{IV\@. Requirements on modified works} All modified versions of documents covered by this license, including translations, anthologies, compilations and partial documents, must meet the following requirements: \begin{itemize} \item The modified version must be labelled as such. \item The person making the modifications must be identified and the modifications dated. \item Acknowledgement of the original author and publisher if applicable must be retained according to normal academic citation practices. \item The location of the original unmodified document must be identified. \item The original author's (or authors') name(s) may not be used to assert or imply endorsement of the resulting document without the original author's (or authors') permission. \end{itemize} \subsection*{V\@. Good-practice recommendations} In addition to the requirements of this license, it is requested from and strongly recommended of redistributors that: \begin{itemize} \item If you are distributing Open Publication works on hardcopy or CD-ROM, you provide email notification to the authors of your intent to redistribute at least thirty days before your manuscript or media freeze, to give the authors time to provide updated documents. This notification should describe modifications, if any, made to the document. \item All substantive modifications (including deletions) be either clearly marked up in the document or else described in an attachment to the document. \item Finally, while it is not mandatory under this license, it is considered good form to offer a free copy of any hardcopy and CD-ROM expression of an Open Publication-licensed work to its author(s). \end{itemize} \subsection*{VI\@. Licence options} Distribution of substantively modified versions of this document is prohibited without the explicit permission of the copyright holder. Distribution of the work or derivative of the work in any standard (paper) book form is prohibited unless prior permission is obtained from the copyright holder. \subsection*{Open Publication policy appendix:} (This is not considered part of the licence.) Open Publication works are available in source format via the Open Publication home page at: \begin{quote} \texttt{http://works.opencontent.org/}. \end{quote} Open Publication authors who want to include their own license on Open Publication works may do so, as long as their terms are not more restrictive than the Open Publication license. If you have questions about the Open Publication License, please contact David Wiley, and/or the Open Publication Authors' List at: \begin{quote} \texttt{opal@opencontent.org} \end{quote} , via email. To subscribe to the Open Publication Authors' List send eqmail to: \begin{quote} \texttt{opal-request@opencontent.org} \end{quote} with the word ``subscribe'' in the body. To post to the Open Publication Authors' List send email to: \begin{quote} \texttt{opal@opencontent.org} \end{quote} or simply reply to a previous post. To unsubscribe from the Open Publication Authors' List send E-mail to: \begin{quote} \texttt{opal-request@opencontent.org} \end{quote} with the word ``unsubscribe'' in the body. \section*{The Bit at the Beginning}\addcontentsline{toc}{section}{The Bit at the beginning} \index{acknowledgements} \subsection*{Acknowledgements} Thanks to Leanne Wiedemann and to various members of the Institute of Cancer Research for reviewing this book---special mention to Ken Merrifield, Kim Harrison-Lavoie and Gillian Hynes who'd better both credit me in their theses. Thanks to Renate Divers, Chris Marshall, Phil Martin and Keith Willison. A round of Tubby Toast to Dr Asperger. Thanks as usual to Mrs May Townsend. Thanks to others who have offered suggestions and corrections since the book was first made available. I now work at the Human Genome Mapping Project Resource Centre in Cambridge, UK. The Director, Duncan Campbell, has kindly made copies of Word for the Wise available to students here too. Thanks to him and to Pauline Finbow for organizing this. \index{disclaimer} \subsection*{Disclaimer} The edition you are reading is version 3.0 (August 2002). It contains errors of fact and execution, but fewer than version 2.2. If you find another mistake, don't blame any of the people above---it's my fault. Please tell me and I will do my best to fix it. This book contains opinions. Just like the errors these are mine. They are even less likely to be accurate than the ``facts''. If you are writing to an official specification or working under supervision follow your authority and not my advice. If you have a mind of your own you should use that first. \index{notation!used in this guide} \subsection*{A Note about notation} Though I have tried to be consistent in describing commands let me know when I fail. \index{fonts!used in this guide} \subsubsection*{fonts} The more general and discursive passages in the text appear in this normal text font, ``Utopia''. \begin{sffamily} \begin{itemize} \item Instructions to perform particular actions appear itemized in Helvetica like this\ldots \end{itemize} \ldots with additional explanations below in blocked Helvetica like this. In both cases, specific commands are e\textbf{bold}ened and, usually, \textbf{Capitalized} too, as they appear in the program itself. \end{sffamily} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} } \begin{sffamily} \noindent \rule{\linewidth}{1pt} Mac instructions are marked with a MacOS icon like this box is. I assume you have versions 6.x or 98-. Some of the commands I'll describe are absent or different in versions 5.x. I have tried to provide alternate information for version 5 users where I can. \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Windows\\ \includegraphics[width=1.0cm]{winlogo.eps} } \begin{sffamily} \noindent \rule{\linewidth}{1pt} PC instructions are marked with a Windows icon like this box is. I assume you are using Word 7 (also known as Word 95), 97 or 2000. Most of the commands should work with version 6. \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{keyboard terms} \index{keyboard!terminology} \index{keyboard!layout} \label{Keyboards} I assume you have a modern ``extended'' keyboard with a full complement of control and number keys, though I try to cater for you if you have a simpler set-up. A modern keyboard should carry a\ldots \paragraph*{\ldots Qwerty keypad.} \index{keyboard!Qwerty keyboard} \index{keypad!Qwerty keypad} \index{Qwerty keyboard} This is the main block with all the letters of the alphabet and punctuation symbols on it and a\ldots \paragraph*{\ldots Numeric keypad.} \index{keyboard!Numeric keypad} \index{keypad!Numeric keypad} \index{Numeric keypad} This is the block of 11 or 17 keys on the right hand side. \paragraph*{Extended keyboards} \index{Extended keyboard} should also have small clusters of cursor control (arrow), page navigation and screen keys, between the two main key blocks, possibly plus function keys ranged across the top. \subsubsection*{the modifying keys} \index{modifying keys} \index{keys!modifying} With Word there is a variety of commands available directly from the function keys, but you can use the most common options by holding down the ``\textbf{Command}'' key in combination with a ``memorable'' letter key. On PCs this \textbf{Command} key is called \textbf{Control} (labelled ``CTRL''), on Macs it's the Apple key (labelled \includegraphics[width=0.3cm]{cloverleaf.eps}). For example, you can \textbf{Save} the current document without choosing \textbf{File $\mid$ Save} from the menu bar. Instead you just hit \textbf{Command-S}. On a PC that's ``CTRL-S'', on a Mac ``\includegraphics[width=0.3cm]{cloverleaf.eps}-S''. I save time in the main text by referring to these combinations as ``\textbf{Command-X}'' (or whatever the relevant letter is). (See page \pageref{CommandKeyShortcuts} for more details.) \subsubsection*{menus} \index{notation!menu notation} When you need to choose a command from a menu, I quote the caption on the main, ``parent'', menu or window first. I follow this with a vertical bar then the caption of the option you should choose next. For example, instead of asking you to pull down the \textbf{File} menu from the top toolbar and choose \textbf{Edit} from the resulting sub-menu, I write: \begin{sffamily} \begin{itemize} \item Choose {\textbf{File $\mid$ Edit}.} \end{itemize} \end{sffamily} \tableofcontents \mainmatter \setcounter{chapter}{0} \chapter{Before you start} \section*{Read me first}\addcontentsline{toc}{section}{Read Me} What is the point of spending over a hundred pounds and enduring an epic installation process if you are just going to use Word as a glorified typewriter? Using this package on a modern computer you can plan out any large creative work. It will generate contents pages automatically and format equations. Later versions of the program can correct your spelling and, less successfully, your grammar. (With a good reference management add-on) Word can also save you vast amounts of time in preparing bibliographies. Once you have written and formatted your document you can globally search and change its content and appearance. All of these tasks are surprisingly easy given two things: someone around to save you learning how to do them the hard way and a sense of Word as a way of \emph{structuring} your documents---not as a box of tricks for tarting them up. This approach improves the quality of your work in a deeper way; it encourages you to structure your \emph{thinking}. \subsection*{What you need to begin} \index{assumed knowledge}\index{prerequisites} I assume that you: \begin{itemize} \item can find your way around a graphical interface like MacOS or Windows, know how to point-and-click, select from menus and open, close and save files, \item are nimble enough to manage combinations like ``shift-clicks'' (holding down the `shift' key and clicking a mouse button simultaneously) and ``double-clicks''. \end{itemize} If you aren't familiar with any of these techniques ask someone who is now! \subsection*{What it's all about} \index{aims of guide} This book aims: \begin{itemize} \item to teach you some useful tricks with Word. These will save you time and make writing a great deal more enjoyable. \item to be a permanent portable reference. I have gathered together some of the stuff that I have found most relevant to word-processing anything bigger and more technical than a letter to your bank. \item to suggest some productive approaches to writing. It's not just your technique that matters---it's your attitude. \end{itemize} \subsection*{What it's not} This book isn't: \begin{itemize} \item a guide to getting a PhD. \item another ``Dummies' Guide''---my first (and biggest?) assumption is that you aren't a dummy. \item neglectful of academic or scientific features---the sort of features most commercial guides to using Word tend to ignore. \item packed with page-filling screen-shots. Instead of looking at pictures of the program in action you should work through this book with a real copy of Word running on a computer in front of you. The best way to learn is by doing, so example Word files accompany the text. These are available on disk or to download. \end{itemize} \section*{The first tip}\addcontentsline{toc}{section}{The First tip} \paragraph{Don't work from a floppy.} \index{floppy disk!working from} When using a shared computer, many people work with their document on a floppy disk. This may seem a sensible way for them to avoid damaging their own, original, copies of their work, but it isn't. Word loves to read and write from the current file on disk while you edit. Even a very fast computer can only swap information slowly with a floppy drive---hard drives are, in contrast, almost always high speed devices. Before it prints, Word saves a temporary copy of the entire document to the local disk. A floppy disk may overflow with a large document or the process may crash the machine. It's smarter to copy your current document to your machine's hard disk drive \emph{before} you open Word. While you are working, of course, it is very sensible to \index{backing up}\index{back-up copies}back up the document from time to time to a floppy disk and/or a shared ``file server'' (a powerful remote computer networked to yours for storage purposes) (see ``Using file servers'', page \pageref{UsingFileServers}). If you are using MacOS or Windows 95-, the best place for the current working document is on your computer's ``desktop'': \section*{TRY\ldots WORKING FROM THE HARD DRIVE}\addcontentsline{toc}{section}{\textit{Try working from hard drive}} \index{hard drive!working from} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} } \noindent \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Insert the floppy disk and wait for the disk icon to appear on the desktop. \item If it doesn't open itself, double-click the floppy disk icon and locate your document in the new window. \item Now select the icon for your document and move it over the desktop, holding down the `alt' key as you use the mouse. \end{itemize} Using the mouse button and the `alt' key together \emph{moves} rather than \emph{copies} the file. \begin{itemize} \item Double-click the new desktop copy to \textbf{Open} the document into Word. \end{itemize} \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Win\\ \includegraphics[width=1.0cm]{winlogo.eps} } \begin{sffamily} \noindent \rule{\linewidth}{1pt} \vspace{0pt} \begin{itemize} \item Insert the floppy disk. \item \textbf{Open} the document in Word. \item Choose \textbf{File $\mid$ Save As}. \item \textbf{Save} the document to a directory on your C: drive (Windows 3.x) or desktop (Windows 95-). \item Continue working from this version on the hard drive. \end{itemize} \noindent \rule{\linewidth}{1pt} \end{sffamily} \chapter{Don't write---build} \index{begin!how to} \section*{Use a dirty rag}\addcontentsline{toc}{section}{Use a dirty rage} The hardest thing is starting. Leonardo da Vinci, like all perfectionists, is supposed to have found it so difficult to make the first brushstroke of a painting that he would take the cloth he had used to clean his brushes the previous day and sling it at the empty canvas. Once that was out of the way he could get on with the \textsl{Mona Lisa}, the \textsl{Last Supper} or whatever little job he was working on without agonising over how to begin. There is a very high activation energy to documenting research which I hope the following suggestions will lower significantly. \section*{Writer's block}\addcontentsline{toc}{section}{Writer's block} \index{writer's block!cures for} The first thing to do then is just to write something! When you find that you can't there are several effective tricks you could try. Here are three that have worked for me at one time or another: \subsection*{Explain it to your parents} If your parents are experts in your field, imagine instead that you are summarising your work for other lay people you know well. This is good for structure; it is a useful way to take a complete overview of what you plan to say. It is good for style; it forces you to simplify your language. It is good for your reasoning; you will need to think of how you might justify your approach to another person. If nothing else, this exercise will show you which parts of your work you understand well enough to translate into plain English and which parts you don't. \subsection*{Pretend you are stupid} When starting to write, many people suffer from feelings of ignorance or self-doubt: ``what do \emph{I} know about cell biology? I can't write this.'' Try reverse psychology: ``Cell biology is mostly a mystery to me, but one thing I \emph{do} know about [say] the nucleus is\ldots'' \subsection*{Answer a question} It's often been said that an article, thesis or book is an attempt to answer a question. In science the question is often: ``what did you do and what happened when you did it?''. If that question seems to big too you, break it down into smaller questions. For example, good place to start is ``what did you do first?''. By the time you recount your attempts the question may have changed, but the tale should be worth telling. If the answer to the question is long enough, it becomes a ``story''. You introduce your ``characters'': the current issues, models or techniques. You follow them through your work, and reach the ``moral'' in your conclusion. When you are preparing a scientific paper the stages in this progression have been formalised in the ``notes to authors'' provided by the publishers. In this case you don't have to think of the headings for your ``chapters'' because the broad structure of the finished document has been specified for you. I can't say often enough that structure is the secret of good writing. \section*{Revising is easier than creating}\addcontentsline{toc}{section}{Revising easier than creating} As Leonardo demonstrated, if you have some material to work on, however meagre, you have a start. The best kind of start is a framework rather than a filling. If you have arranged things in a logical way beforehand not only will it be easier to complete your writing, but formatting the finished result with Word will be a faster and more enjoyable process, provided you remember to\ldots \section*{Mark up content, not appearance}\addcontentsline{toc}{section}{Mark up content, not appearance} Up until now you should have been thinking of your story---not the exact way you will tell it. Writer's block frequently comes from squinting at tiny details before surveying the bigger picture. This panoramic approach is also perfectly suited to the way Word and other professional text-handling programs mark up text for formatting. When I say ``mark up'' I mean the way that you will label the structure of your document. Step back from your writing and see its content as a hierarchy of different levels of importance, rather than pressing your face up against your current sentence and asking yourself whether the surrounding paragraph looks best in ``bold''. If you see text mark-up as a cosmetic exercise, to be performed as you write, what will happen when you decide that all 43 sub-headings look stupid in the font you've chosen? Schlepp through the whole thing finding and changing them?\footnote{A smart reader of an earlier version of this book (thank you, Gillian Hynes) pointed out to me that there is a way around this problem---see ``Styles without content'', page \pageref{StylesWithoutContent}.} \section*{TRY\ldots TO GET A FEEL FOR THE TOOLS}\addcontentsline{toc}{section}{\textit{Try to get a feel for the tools}} \index{tools!getting a feel for} \begin{sffamily} Throughout I'll try to give advice to cover your particular copy of Word, whether you are running it under MacOS or on a PC under Windows. Usually the differences are small and I'll just describe the different ways of selecting the same commands in successive lines. \end{sffamily} \section*{Mac and Windows instructions}\addcontentsline{toc}{section}{Mac and Windows instructions} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} } \begin{sffamily} \noindent \rule{\linewidth}{1pt} Mac instructions are marked with a MacOS icon like this box is. I assume you have versions 6.x or 98-. Some of the commands I'll describe are absent or different in versions 5.x. I have tried to provide alternate information for version 5 users where I can. \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Windows\\ \includegraphics[width=1.0cm]{winlogo.eps} } \begin{sffamily} \noindent \rule{\linewidth}{1pt} PC instructions are marked with a Windows icon like this box is. I assume you are using Word 7 (also known as Word 95), 97 or 2000. Most of the commands should work with version 6. \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsection*{Mac and Windows interfaces} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} } \index{interface!Word under MacOS} \begin{sffamily} \noindent \rule{\linewidth}{1pt} Microsoft Word for MacOS opens with the usual \textbf{Apple Menu} at the top of the page. There you will find text headings for the sub-menus: \textbf{File}, \textbf{Edit}, \textbf{View} and so on. Immediately below the \textbf{Apple Menu} you'll find the \textbf{Standard Toolbar} with icon buttons for frequent actions like opening a new document. Next is the \textbf{Formatting Toolbar} with drop-down menus for formatting and font styles as well as the \emph{evil} \textbf{Bold} button---later you'll understand why I disapprove. Check for all of these above the ``\textbf{Music Bar}'', the lined frame segment at the top of the current window carrying your document's name. It is so called after its resemblance to a musical staff. \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Win\\ \includegraphics[width=1.0cm]{winlogo.eps} } \index{interface!Word under Windows} \begin{sffamily} \noindent \rule{\linewidth}{1pt} At the top of the Word for Windows screen there is the name of the program itself and of the document you are currently working on. Below that is the \textbf{Menu Bar} with menu heads like \textbf{File}, \textbf{Edit} and \textbf{Tools}. Next, the \textbf{Standard Toolbar} carries buttons with icons representing frequently-used commands. ``Pressing'' these with the mouse pointer instructs the program to do things like create new documents, cut or paste selected text and save files. I'm going to assume you are familiar with the basics of these parts of the interface and their use and move to the less familiar bits of the \textbf{Formatting Toolbar}, the fourth level down from the top of a normal Word window. \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsection*{Showing toolbars} \index{toolbars!showing} \begin{sffamily} If you can't see the \textbf{Standard} or \textbf{Formatting Toolbars}\dots \begin{itemize} \item \dots choose \textbf{View $\mid$ View Toolbars} and click a cross in the appropriate box of the menu. These are referred to as ``checkboxes''. \end{itemize} Naturally, selecting and de-selecting such options is done by ``checking'' (putting a cross in the relevant box by clicking) and ``un-checking'' (clicking inside the relevant box to remove a cross). Most people know how to use the \fbox{\textbf{B}} and \fbox{\textit{I}} buttons to obtain \textbf{bold} and \textit{italic} text respectively and the justification boxes for left- and right-justified text, for example, but there are other parts of the \textbf{Formatting Toolbar} that are less commonly used. These neglected tools are far more effective than their better-known cousins. Open a document and investigate them. \end{sffamily} \section*{TRY\ldots EXAMINING A STRUCTURED DOCUMENT}\addcontentsline{toc}{section}{\textit{Try examining a structured document}} \index{structured document!how to view} \begin{sffamily} \index{structured document!example} A couple of ready-made documents should accompany this manual to save you time and typing. They are available for download in various formats if not present on disk. Contact the author for details if necessary. The main text of these samples is public-domain Latin from the works of Libellus. Only the headings are in English. If you have \textbf{Automatic Spell Checking} on when you open them you'll find that the Latin words are almost all underlined in red. Your spell checker will probably choke and display a message about there being too many errors to mark. \begin{itemize} \index{structured document!viewing} \index{view!document views} \index{document views} \item \textbf{Open} the document ``LIFE''. \item \index{view!\textbf{Normal} View}If you aren't already using \textbf{Normal} view, choose \textbf{Normal} from the \textbf{View} menu. \item Scroll through the document to get a feel of the overall layout. \end{itemize} The headings have been chosen to make clear the structure of the document---from the highest level of description defined: the title of the document, ``Life, The Universe and Everything'', to the lowest: ``Kilburn''. You may well have used the \textbf{Normal} or \index{view!\textbf{Layout} View}\textbf{Layout} views before, but you will find that, even for a relatively small section like this, the \index{view!\textbf{Outline} View}\textbf{Outline} and \index{view!\textbf{Master Document} View}\textbf{Master Document} views are far more useful for seeing the structure of the document. \begin{itemize} \item Go back to the \textbf{View} menu and choose \textbf{Outline}. \end{itemize} As you can see, the document immediately takes on a staircase appearance, with the highest levels of organisation leftmost, staggering down toward the body text blocked to the right. The power of this view shows when you use the new \textbf{Outlining / Master Document Toolbar} that has appeared---either floating above the document or at the top of the document window. \begin{itemize} \item On the \textbf{Master Document Toolbar} click on the button marked \textbf{4} \end{itemize} By doing this you have chosen to display only the four highest levels of organisation, from \textbf{Heading 1} level down to \textbf{Heading 4}. \begin{itemize} \item Watch the body text collapse into thin grey lines between the third-level headings. \end{itemize} The logical plan of the entire document is immediately clear. \begin{itemize} \item Cycle through the various \textbf{View} options: \textbf{Normal}, \textbf{Outline}, \index{view!\textbf{Page Layout} View}\textbf{Page Layout} and, if available, \textbf{Master Document}. \end{itemize} \begin{itemize} \item Notice that the main difference between the \textbf{Outline} and \textbf{Master Document} views is that the end-of-section divisions are hidden in the \textbf{Master Document View}. \end{itemize} This is truly the ``logical'' view of the document, stripped almost entirely of information about the document's actual appearance on paper. \begin{itemize} \item Now open the document ``DEATH'' and try the same thing. \end{itemize} Nothing much happens. So marking up your document with levels of organisation, instead of font sizes and appearances, makes it the document's structure more obvious. Things get \emph{really} interesting when you come to format your work. \end{sffamily} \section*{TRY\ldots MAKING A CONTENTS TABLE INSTANTLY}\addcontentsline{toc}{section}{\textit{Try making a contents table instantly}} \begin{sffamily} \begin{itemize} \item Switch back to the file ``LIFE''. \item Choose \textbf{View $\mid$ Normal}. \end{itemize} \end{sffamily} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} version 5-} \index{contents!table of!how to insert!Mac} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item If you aren't already there, move to the beginning of the document by pressing \includegraphics[width=0.3cm]{cloverleaf.eps}-Home. (See below if you don't have a ``Home'' key.) \end{itemize} The \textbf{Home} key is normally one of a small keypad to the right of the main qwerty cluster. On the Mac, instead of being labelled ``Home'', it probably carries an arrow pointing upward and to the left: $\nwarrow$, indicating the ``top left'' of the entire document.) Some Macs don't have this key. You will find that this and other commands normally found on the extended keyboard can be emulated with keys on the numeric keypad. In this case, use \includegraphics[width=0.3cm]{cloverleaf.eps}-5 (that is, ``5'' on the numeric keypad, rather than the one on the keyboard proper). (See ``Keyboards'' in the introduction, page \pageref{Keyboards}, for descriptions of keyboard terminology.) \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Win\\ \includegraphics[width=1.0cm]{winlogo.eps} version 6-} \index{contents!table of!how to insert!Win 6-} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Find your way to the beginning by pressing \textbf{CTRL-Home}. \end{itemize} You may previously have used the \textbf{Home} key on its own to move to the beginning of a line. It's normally one of a small keypad to the right of the main ``qwerty'' cluster and the left of the numeric keypad. (See ``Keyboards'' in the introduction, page \pageref{Keyboards}, for descriptions of keyboard terminology.) \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} version 5} \index{contents!table of!how to insert!Mac 5} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Now choose \textbf{Insert $\mid$ Table of Contents}. \end{itemize} When you click \textbf{Start} a formatted table of contents will appear automagically. \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{both\\ \includegraphics[width=0.50cm]{maclogo.eps} \includegraphics[width=0.66cm]{winlogo.eps} version 6-} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Now choose \textbf{Insert $\mid$ Index and Tables}. \end{itemize} The \textbf{Index and Tables} dialogue box will appear. \begin{itemize} \item Click on the tab marked \textbf{Table Of Contents}. \end{itemize} The following boxes should be checked: \textbf{Show Page Numbers} and \textbf{Right Align Page Numbers}. The \textbf{Show Levels} box should show the number \textbf{3}. (Next, if you like, you can use the \textbf{Tab Leader} box to choose whatever kind of dots you want to appear between each content heading and its corresponding page number.) \begin{itemize} \item Choose \textbf{Classic} from the \textbf{Formats} box and click \textbf{OK}. \end{itemize} \noindent \rule{\linewidth}{1pt} \subsubsection{instant contents!} Tah-dah! Your document now has a complete and up-to-date table of contents. Not only did it take just three commands and no typing from you, but, if you modify the structure of your document or change any of its headings or page numbers, you can update the contents page completely automatically to reflect your changes. In later versions of Word you can just highlight the contents and press \fbox{F9}. Otherwise just \textbf{Insert} a new table of contents over the original. \end{sffamily} \section*{TRY\ldots STRUCTURING A DOCUMENT YOURSELF}\addcontentsline{toc}{section}{\textit{Try structuring a document yourself}} \index{structured document!how to make a} \index{document!how to structure} \begin{sffamily} \subsubsection{a rescue job} Now you're going to take the document ``Death''---a perfect example of how \emph{not} to do it---and knock it into the well-structured shape of ``LIFE''. It's best to start from scratch and discard all of the original author's dodgy formatting. This is done by saving the content of the document---the text alone. Remember that this would be a dangerous approach if there were lots of special characters present, but we want to Keep It Simple at this stage. \begin{itemize} \item Open ``DEATH''. \item Choose \textbf{File $\mid$ Save As}. \item Choose a sensible place to save it---the desktop if your computer's operating system has one. \item Type in the name ``STRUCT''. \item From the drop-down \textbf{Save File as Type} or \textbf{File Type} box that appears below choose \textbf{Text Only} before clicking \textbf{OK} or \textbf{Save}. \end{itemize} Saving the document as a separately named file has the added advantage that you keep the original in its initial hopeless state---just in case someone else was daft enough to want it that way. \begin{itemize} \item If necessary, \textbf{Close} the original ``DEATH'' document. \item (Choose \textbf{No} if you are asked about saving formatting information.) \end{itemize} \subsubsection{logical formatting} \index{formatting!logical} \index{format!styles!how to} \index{styles!how to format} You can now re-open your text-only version and begin to apply \emph{logical} formatting to your own version, starting with the main title. \begin{itemize} \item Again, only if necessary, \textbf{Open} the ``STRUCT'' document. \end{itemize} You may need to set the \textbf{File Type} to \textbf{All Files} to be able to browse the file. \begin{itemize} \item If you are asked for a file type to convert from choose \textbf{Text Only}. \item Select the first line, the title. \end{itemize} \index{cursor!moving} You probably did this by dragging the mouse along the entire first line, ``Death, Decay and Damnation''. Why not try a quicker method? \begin{itemize} \item Start with the cursor in the middle of any paragraph. \item Without clicking, carefully move the mouse pointer until it's level with the left edge of the title line. \item Slowly move the cursor towards the left edge of the page. \item Stop at the moment when the cursor turns into an arrow pointing upwards and to the right. \item Click the (left) mouse button once. \item The entire title line should now be highlighted. Now you can apply your first bit of logical formatting. \end{itemize} \end{sffamily} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} version 5} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Press \textbf{\includegraphics[width=0.3cm]{cloverleaf.eps}}-\textbf{T} (\textbf{Format $\mid$ Style}). \end{itemize} \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{both\\ \includegraphics[width=0.50cm]{maclogo.eps} \includegraphics[width=0.66cm]{winlogo.eps} version 6-} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item \index{style!Word's styles}Go to the \fbox{$\bigtriangledown$} arrow to the right of the \textbf{Style} box. \end{itemize} The \textbf{Style} box is the rectangular window on the left of the \textbf{Formatting Toolbar}. It probably says \textbf{Normal} at the moment. \begin{itemize} \item Click it and the list of formatting styles will drop down. (This is why such controls are called ``drop-down boxes''.) \end{itemize} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Highlight the \textbf{Heading 1} option and click it. \end{itemize} The first line has now been formatted using the default (Normal template) \textbf{Heading 1} style. This is the only line that you will mark up at this level. Next you can format the following sub-heading in style \textbf{Heading 2} using the same technique. \begin{itemize} \item Move the cursor to the margin adjacent to the sub-heading ``DEATH''. \item Select the entire line. \item Use the same commands as before, but choose \textbf{Heading 2} from the \textbf{Styles} box. \end{itemize} \begin{itemize} \item Do the same for the other second-level headings. These are ``Decay'' and ``Damnation''. \end{itemize} You can move to the next layer of the hierarchy of this document and format ``Popping Your Clogs'', ``Waving Bye-Bye'', ``Kicking The Bucket''. ``Going Stiff'' and so on as the next level of organisation\ldots \begin{itemize} \item Format these lines in style \textbf{Heading 3}. \end{itemize} \subsubsection{repeat command} There is an excellent short-cut to repeat the last command you used which will be handy here and in many other situations. In this case you want to format some text to \textbf{Heading 3} style. After you have applied \textbf{Heading 3} formatting once\ldots \end{sffamily} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} version 5-} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Format your next \textbf{Heading 3} by using: \includegraphics[width=0.3cm]{cloverleaf.eps}-Y (correctly, \textbf{Command-Y}). \end{itemize} \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Win\\ \includegraphics[width=1.0cm]{winlogo.eps} version 6-} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Format your next \textbf{Heading 3} by using \textbf{CTRL-Y} (that is, \textbf{Command-Y}). \end{itemize} \noindent \rule{\linewidth}{1pt} \end{sffamily} \begin{sffamily} \subsubsection{normal text} OK, so you understand how to select and format heading lines, now you can tackle one paragraph of ``Normal'' or ``Body'' text. \begin{itemize} \item First move back to the very start of the document. If you remember the previous ``how-to'' you can do this without using the mouse. \item Now move the mouse pointer to the left margin of any line in the first paragraph. \end{itemize} This paragraph begins with the line: ``Item statutum est quod omnes habitantes extra portas bugelle.'' \begin{itemize} \item As the cursor becomes a ``north-east'' arrow, double-click the (left) mouse button. \end{itemize} This should select the entire paragraph. \begin{itemize} \item This time format the selection with the style \textbf{Normal}. \end{itemize} The paragraph was probably already in \textbf{Normal} style so you can skip doing this for the other paragraphs in the document. If necessary you can repeat it for the other paragraphs using the ``repeat last command'' trick from earlier. \end{sffamily} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} version 5} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \textbf{Word for Mac version 5 users stop here and go to chapter 3!} \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{both\\ \includegraphics[width=0.50cm]{maclogo.eps} \includegraphics[width=0.66cm]{winlogo.eps} version 6-} \begin{sffamily} \noindent \rule{\linewidth}{1pt} There is a much surer way to go about this whole process, but it's less educational. Instead of picking your way between the headings, changing all the paragraphs of normal text individually, a more sensible first step is to put the whole document in \textbf{Normal} style and convert the headings to their various levels afterwards. When you have logically formatted the entire document, try the different options available from the \textbf{View} menu. Check that the appearance of your modified ``DEATH'' document compares with the original, pre-formatting ``LIFE'' document under \textbf{Outline} view with button \textbf{4} on the toolbar pressed in, for example. You won't be surprised to learn that there is a much less tedious way of converting style mark-up to content mark-up for a whole document (see ``Styles without content'', page \pageref{StylesWithoutContent}.) \index{contents!table of!changing style} Finally, if you have version 6 or later, generate two versions of the document with tables of contents in entirely different styles. Try one with a \textbf{Modern} style and show only the top two levels of heading. Then try another in \textbf{Elegant} style showing all levels of mark-up. The other great value of this approach is that you can globally change the appearance of all the level 2 headings in your document, in one step. You can use either a built-in Word template or you can specify exactly how you want your text to appear at various heading levels. As a simple example, let's say that, now we have reformatted ``DEATH'' sensibly we don't like the look of the \textbf{Heading 1} font chosen by Word. \noindent \rule{\linewidth}{1pt} \end{sffamily} \section*{TRY\ldots REDEFINING A STYLE}\addcontentsline{toc}{section}{\textit{Try redefining a style}} \index{styles!Word styles!how to redefine} \begin{sffamily} \begin{itemize} \item Go back to \textbf{Normal View}. \item Put the cursor in the middle of a line of \textbf{Heading 1} text. \item Choose \textbf{Format $\mid$ Style}. \item Click \textbf{Modify}. \item In the new window that appears, choose \textbf{Font} from the \textbf{Format} drop-down box. \end{itemize} Now you can select any other font in any other size or appearance and all \textbf{Heading 1} text in the document will appear in that style forever after. (When you've chosen a new font, it may well pay to click in the ``Automatically update'' box if it's present.) After you have closed all the windows you can examine the effect of your changes on the document. You can repeat this approach for any and all of the different text styles available until you have a combination of characteristics that pleases you. Note that when you do this for the \textbf{Normal} style it often turns out to be the basis for all the other styles so if, for example, you set the \textbf{Normal} style to be set in the ``Garamond'' font, your \textbf{Heading} styles may all turn to Garamond too. This behaviour varies from template to template. For more about templates read on\ldots \index{template!document templates} \subsection*{Word's built-in templates} Some of the pre-defined templates are very good, however. They include lots of subtle but effective attributes like well-chosen line-spacing above and below Headings (\textbf{Format $\mid$ Style $\mid$ Modify $\mid$ Format $\mid$ Paragraph}). This is easier and more precise than your manually inserting carriage returns. Also in the \textbf{Format $\mid$ Style} window you can make a Heading style, say, switch automatically to a \textbf{Normal} style when you move start the next paragraph using the ``\textbf{Style for following paragraph}'' box. Experiment! If you have a later version of Word and you'd like a more dramatic demonstration of global formatting\ldots \begin{itemize} \item \ldots choose \textbf{Format $\mid$ Style Gallery} and explore the effect on all levels of the text of choosing one of the different document styles provided. Click on any template you fancy in the left-hand panel. \end{itemize} There is also a (U.S.-style) thesis template available for download from the Microsoft site: \begin{quotation} \texttt{http://www.microsoft.com} \end{quotation} \end{sffamily} \chapter{Pitfalls} \index{pitfalls!mistakes with Word} \section*{The dangers of defaults}\addcontentsline{toc}{section}{The Dangers of defaults} \index{default settings!dangers of} A ``default'' is the choice you get when you don't make a choice. Most of the time the defaults Word chooses for you are perfectly sensible. This, and laziness, can tempt you to accept Word's defaults all the time. Often the results aren't quite what you intended. A frequent reason for disappointment is that Word was originally written for U.S. customers. \subsection*{A4 / letter} \index{paper size!setting} \index{A4!paper size in \textbf{Page Setup}}A classic example of this is the U.S. office preference for so-called ``letter paper''. It's important to choose the right \textbf{Paper Size} settings from the \textbf{File $\mid$ Page Setup} dialogue box or other characteristics such as margins will be calculated on (usually false) assumptions about the dimensions of the paper in your printer. \subsection*{U.S. Dictionary/Thesaurus} \index{\textbf{Options}!setting up your options} \index{dictionary!setting} \index{dictionary!English or American} \index{UK English!dictionary} Americans can't spell English so, before you even think about using the spell checker, choose \textbf{Tools $\mid$ Options $\mid$ Spelling} and make sure that the options set are the ones you really want. (Of course you may be preparing a paper for publication in a U.S. journal and want a U.S. dictionary.) It's also a good idea to click in the \index{custom dictionary}\index{dictionary!\textbf{Custom Dictionary}}\textbf{CUSTOM DICTIONARY} box so that you can add your own (specialised or scientific) vocabulary to the dictionary as you spell check your document. You may also have to select the entire document ---\textbf{Edit $\mid$ Select All}---and adjust the \textbf{Language} setting under \textbf{Tools $\mid$ Language $\mid$ Set Language}. \subsection*{``Big Brother''---the Edit/AutoCorrect options} \index{\textbf{AutoCorrect}} The more recent editions of Word boast some quite maddening ``features'' designed to catch errors in your work on the fly. Perhaps, as you have been using one of these versions, you have noticed red lines appear under words the program considers misspelt. This continuous spell-checking can be a royal pain to regular users, but is especially unsuited to scientific work. Scientific writing inevitably contains neologisms (clathrin, coatomer), and acronyms (Mabs, Fabs and SNAREs). Such odd combinations of letters and cases are guaranteed to upset the \textbf{AutoCorrect} and \textbf{Spelling} routines. You might find it helpful to keep your own \index{dictionary!custom}\index{custom dictionary}custom dictionary and \textbf{Add} new words unrecognised by the built-in dictionary when you run a spell check. I also find it's easiest to turn off \textbf{Automatic Spell Checking} and certain \textbf{AutoCorrect} features while writing. When my attention begins to wander, after half-an-hour or so, I run a manual spelling check to amuse myself. \section*{Back it up, back it up, back it up}\addcontentsline{toc}{section}{Back it up, back it up, back it up} \index{backing up} \index{back-up copies} You will hate yourself forever if you destroy your only copy of your work. I know it's boring, but there are only three ways around this: back it up, back it up or back it up. It's not enough to save your document three times to the same hard-disk drive or to make several floppy disk duplicates and waste the effort of doing so by keeping them in the same physical location. The whole point of a back-up copy is that, when your original is destroyed by a volcano in Montserrat, the duplicate is safely untouched in Catford. \subsection*{Get ahead---get a schedule} \index{backing up!schedules} \index{schedule!for back-ups} The other sad truth about back-ups is that your hard disk only ever fries itself ``just before you were about to back everything up''. Funny that. The best way to avoid finding your last back up was made during the Cretaceous period is to have a back-up schedule. Make yourself a new separate back-up at the end of every day. It only takes a moment, whereas rewriting your lost work takes twice as long as it did the first time round. Paranoid users tend to take this too far and work with their current document on a \index{floppy disk!working from}floppy disk for fear that someone will erase their hard-disk copy. This is probably a mistake. On PCs especially, reading and writing to a floppy disk are slow and occasionally unreliable processes. It's far better to copy your present draft onto the hard disk of your machine and use that as your working copy. Back up both onto a file-server as you go along. Then copy your new version (with a new name---see below) back onto the floppy disk when you've finished a session. \subsection*{A sensible revision policy---simple ``version control''} \index{version control} Until the most recent versions of Word, its tools for maintaining a detailed record of revisions had been pretty poor by comparison with some of the other word-processors on the market. Being able to ``roll back'' changes you have made to restore your work to an earlier state can be very useful in itself, but so-called \index{version!managing versions}\index{version control}``version control'' facilities are even more important when you are working collaboratively on the same paper. Even an individual professor and her secretary can save vast amounts of time with such facilities if, say, one is typing up a review and adding references while the other is revising the main text. Because Word's capabilities in this department have been so limited and the new versions so radically different I am not going to discuss their use in this edition of the guide. Instead I offer a little hard-won advice on maintaining versions of your documents. \index{revisions!naming} \index{versions!naming} \index{version control!policy} Firstly, if you are working on a large project daily, start each day of new work by doing a \textbf{Save As} under a new name, using the same basic title, but a different version number or date. If your computer system supports long filenames you could use something like ``Tarquin's thesis 13Jun98.doc''. If not, you could, for example, number each new working day's draft: \begin{quotation} ``THESIS1A.DOC'', ``THESIS1B.DOC'', ``THESIS1C.DOC'', \end{quotation} changing only the number part of the version each month: \begin{quotation} ``THESIS2A'', ``THESIS2B''. \end{quotation} If you are thinking of making a radical change to the organisation of the document, especially if you are thinking of removing a whole section, you should change the basic name clearly and do a \textbf{Save As}, thereby preserving your original in case things go horribly wrong. Remember, you can't always just hit the \index{\textbf{Undo}!\textbf{Undo} after saves}\textbf{Undo} button after you've done a \textbf{Save}. \subsection*{Using file servers} \index{fileservers!using} \index{backing up!to a fileserver} \label{UsingFileServers}One way to keep your back-up copies separate from your hard-disk originals is to back up your work to a remote computer. If you are working in a networked environment, ask your IT staff about the availability of file-servers. These are machines with a lot of storage capacity, usually administered centrally, but networked in such a way that anyone connected can treat the server as just another disk-drive. You could create a back-up copy of your \textit{magnum opus} as easily as dropping your document's icon onto the file-server icon. The physical network and the software that runs it take care of all the complexities for you. What is even more reassuring about this method is that whoever administers the system should have a strict backing-up schedule for protecting the contents of its file-servers, copying the entire contents of all of their disk-drives to tape and (eventually) storing the tapes off-site. \subsection*{Automatic Save} \index{\textbf{Automatic Save}} In later versions of Word one of the many choices available on the \textbf{Tools $\mid$ Options} menus is the \textbf{Automatic Save} setting. With this you can choose the timing and the types of back-up that Word makes automatically for you while you work---or rather in those moments when you stop working. When you stop typing and stare into space for long enough to trigger this process, it can be irritating having to read the legend: ``Word is autosaving MyThesis.doc'', instead of being able to pick up where you left off, but it's also very reassuring. \section*{TRY\ldots SETTING UP YOUR OPTIONS}\addcontentsline{toc}{section}{\textit{Try setting up your options}} \index{\textbf{Options}!setting up your options} \label{SetUpOptions} \begin{sffamily} \subsubsection{paper size} \index{paper size!setting} \index{page size!setting} First you'll set your paper size. \begin{itemize} \item Choose \textbf{File $\mid$ Page Setup}. \end{itemize} \end{sffamily} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} version 5-} \begin{sffamily} \noindent \rule{\linewidth}{1pt} On a Mac the page size option should be immediately visible, but this depends on the printer you have chosen to use with your machine---check with your Mac or printer manual. \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Win\\ \includegraphics[width=1.0cm]{winlogo.eps} version 6- } \begin{sffamily} \noindent \rule{\linewidth}{1pt} On a PC you should now see a so-called ``tabbed dialogue box''. The tab you are interested in is labelled with the words ``Paper Size''. \noindent \rule{\linewidth}{1pt} \end{sffamily} \begin{sffamily} \begin{itemize} \item Click on the \textbf{Paper Size} or \textbf{Page Size} tab. \end{itemize} Now you can choose the page size you want from the drop down box on the left of this options card. You want A4. On this card you can also fine-tune the dimensions of the paper you are working on and select a \textbf{Landscape} orientation if you want to produce an extended table, say. \begin{itemize} \item Choose \textbf{A4} in the \textbf{Paper Size} drop-down box. \end{itemize} Next you'll make sure your work is backed up in a sensible and reliable way. \end{sffamily} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} } \index{\textbf{Save}!setting options} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Choose \textbf{Tools $\mid$ Preferences} \item Click the \textbf{Open and Save} option in the left-hand pane. \index{\textbf{Fast Saves}!don't allow!Mac} \index{save!save options!Mac} \item Un-check \textbf{Allow Fast Saves}. \end{itemize} \subsubsection{save options} The \textbf{Fast Save} function is notorious as the habitat of some of Word's nastiest bugs. Avoid it at all costs. \begin{itemize} \index{save!save reminder}\item Click the \textbf{Save reminder} box \textbf{on} and choose around 8 minutes. \end{itemize} I find this is a reasonable balance between auto-saving too infrequently to salvage a reasonable amount of lost work and auto-saving too often to allow you to do any work in the first place. \begin{itemize} \item Choose other \textbf{Open and Save} options according to taste. \end{itemize} \subsubsection{on-the-fly options} \index{Options!setting!general} Now you'll look at the \textbf{General} options \begin{itemize} \item In the left pane, select \textbf{General}. \item It may be worth typing in your name and initials here if you don't share the machine with others. \index{\textbf{``Drag-and-drop''!Text editing!}setting} \item Check \textbf{Drag-and-drop Text Editing}. \end{itemize} You'll need this handy feature in the chapter on shortcuts (see ``Mouse shortcuts'', page \pageref{MouseShortcuts}). \begin{itemize} \item \index{\textbf{Smart Quotes}!setting}Put \textbf{Smart Quotes} \textbf{on}. \end{itemize} \index{custom!paper sizes!Mac}In this pane you can also set up custom paper sizes-just in case you want to turn your abstract into an original and educational greetings card. Now you'll\ldots \begin{itemize} \item \index{spelling!setting options!Mac}Select \textbf{Spelling} in the left pane. \item \index{dictionary!choosing UK dictionary!Mac}Choose \textbf{English UK} for the main dictionary. \item In the \textbf{Ignore} box check both \textbf{Words in UPPERCASE} and \textbf{Words with Numbers}. \end{itemize} These sorts of words are both common in science, of course, and you can be reasonably sure that the dictionary doesn't cover them. \begin{itemize} \item Close the window. \end{itemize} \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} version 5} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \textbf{Word for Mac version 5 users stop here and go to chapter 3!} \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{both\\ \includegraphics[width=0.50cm]{maclogo.eps} \includegraphics[width=0.66cm]{winlogo.eps} version 6-} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Choose \textbf{Tools $\mid$ Options}. \item Up pops the \textbf{Options} window. \end{itemize} It is the mother of all tabbed dialogue boxes, carrying at least two rows of tabbed option ``cards'' with labels like \textbf{General}, \textbf{Spelling}, \textbf{Edit} and \textbf{Save}. \subsubsection{save options} \index{save!save options!Win 6-} \begin{itemize} \item Select the \textbf{Save} tab from the \textbf{Options} dialogue box. \end{itemize} This card now moves into the bottom foreground of the window. You can alter (if necessary) the settings so that Word will always create a \index{backing up}\index{back-up copies}backup copy, an entirely separate duplicate file, and so that the program automatically saves the document every 8 minutes. \begin{itemize} \item \index{\textbf{Fast Saves}!don't allow!Win}If checked, un-check the \textbf{Allow Fast Saves} option. \end{itemize} The \textbf{Fast Save} function is a notorious habitat of some of Word's nastiest bugs. Avoid it at all costs. \begin{itemize} \index{save!automatic saves!Win 6-}\item Now check the \index{\textbf{Automatic Save}}\index{\textbf{AutoSave}!setting!Win 6-}\textbf{Automatic Save Every} box. \item And fill the minutes box with the number \textbf{8}. \end{itemize} I find this is a reasonable balance between auto-saving too infrequently to salvage a reasonable amount of lost work and auto-saving too often to allow you to do any work in the first place. \begin{itemize} \item Check and un-check the other boxes according to your preferences. \end{itemize} You may find yourself that the \index{Back-up!setting options!Win 6-}\textbf{Always Create Backup Copy} option is more trouble that it's worth. This is partly because it defaults to saving the backup copy in more-or-less the same place as the original and partly because it gives you a false sense of reassurance when it does. The whole point of a back-up is that it isn't where your original is. \subsubsection{on-the-fly options} Finally you'll deal with some of the more ``anti-science'' \textbf{Edit} and \textbf{AutoCorrect} options. \begin{itemize} \item If necessary, choose \textbf{Tools $\mid$ Options} to bring up the tabbed \textbf{Options} dialogue box again. \item Click on the \textbf{Spelling} tab. \item \index{\textbf{Automatic Spell Checking}!setting options!Win 6-}If there is an \textbf{Automatic Spell Checking} pane un-check the box there labelled \textbf{Automatic Spell Checking}. \end{itemize} You won't be surprised to learn that this turns off \textbf{Automatic Spell Checking}. \begin{itemize} \item Now click on the \textbf{Custom Dictionaries} button and make sure that the default Custom Dictionary, often called CUSTOM.DIC on PCs, has been selected---by checking the adjacent check-box. \end{itemize} You can choose to create a new dictionary and name it after yourself if you like, thereby keeping your own personal vocabulary in separate place. This means that you can ``teach'' the spell-checker to accept specialist terms it doesn't ``know'' by default. When you are running a spell check and the program highlights a word you know to be correct, but the standard dictionary doesn't know at all, just click the \textbf{Add} button. It's a good idea, of course, to check you've spelt it correctly yourself in the first place. \begin{itemize} \item Also check that the drop-down \textbf{Language} box contains \textbf{English UK}. \item Now, after clicking \textbf{OK} to accept our changes you can turn to the \textbf{Edit} tab of the \textbf{Options} window. \end{itemize} \begin{itemize} \index{\textbf{Automatic Word Selection!switching off}}\index{\textbf{Auto Word Select!switching off}}\item Un-check \textbf{Automatic Word Selection}. \end{itemize} \index{select!\textbf{Automatic Word Selection}}This is the feature that makes it so difficult to highlight some of the letters of a word independently of the others---something scientists tend to do often, especially when technical words tend to be so much longer. \begin{itemize} \item Make sure that \textbf{Drag-and-Drop Text Editing} is checked. \end{itemize} This will be essential for the later exercises (see ``Moving a chunk'', page \pageref{MovingAChunk}). \index{\textbf{AutoCorrect}} Next you can tackle \textbf{AutoCorrect} proper. \begin{itemize} \item Choose \textbf{Tools $\mid$ AutoCorrect}. \end{itemize} \index{capitals!turning off autocorrection}The following will suppress the programs over-zealous correction of the various odd forms of capitalisation you are likely to use while writing science. \begin{itemize} \item Un-check \textbf{Correct TWo INitial CApitals}. \item In newer versions of Word you could also un-check \textbf{Correct accidental usage of cAPS LOCK key}. \end{itemize} This final adjustment should drastically reduce ``false positive'' capitalisation errors. \noindent \rule{\linewidth}{1pt} \end{sffamily} \chapter{Shortcuts} \index{shortcuts!general} \section*{Introduction}\addcontentsline{toc}{section}{Introduction} \paragraph{Cultivate a productive laziness.} Shortcuts are key combinations or mouse movements that allow you to manipulate text or select frequently-used commands without stepping through chains of menus with the mouse. With a few shortcuts you can become a great deal more efficient and feel far more in control of Word. Ultimately it's possible reach a stage when the complexities of the program fade and you can concentrate on the task in hand. When users achieve this level of enlightenment their \textit{chakras} glow, bathing those around them in their Buddha-like smugness. \subsection*{Mouse shortcuts} \index{mouse!mouse shortcuts} \index{shortcuts!mouse shortcuts} \index{cursor!moving} \label{MouseShortcuts} These are probably the most important of all; they are certainly the most satisfying to use. It's not so much a question of your remembering any commands, instead you should get a feeling for the way the mouse and its various cursors move and change as you navigate the screen. Armed with a basic ``mouse instinct'' you can avoid a lot of fiddly selecting. \subsection*{Navigation shortcuts} \index{shortcuts!navigation shortcuts} On a modern full PC or Mac keyboard you will find a cluster of six keys between the main Qwerty layout on the left and the numeric keypad on the right. These are labelled with various angled arrows or captions like ``Home'' and ``Page Down''. The ``navigation'' shortcuts I will describe make use of these and the arrow keys, plus various modifying keys like the ``Shift'' and \textbf{Command} keys to help you to surf around your document quickly. The bigger the document the more useful these become. \subsection*{Command key shortcuts} \index{shortcuts!command key} \label{CommandKeyShortcuts} With Word there are a variety of commands available directly from the function keys, but the most common options are available by holding down the \textbf{Command} key in combination with a ``memorable'' letter key. On PCs this \textbf{Command} key is called \textbf{Control} (labelled ``CTRL''), on Macs it's the \textbf{Apple} key (labelled \includegraphics[width=0.3cm]{cloverleaf.eps}). For example, you can \textbf{Save} the current document without choosing \textbf{File $\mid$ Save} from the menu bar. Instead you just hit \textbf{Command-S}. On a PC that's ``CTRL-S'', on a Mac ``\includegraphics[width=0.3cm]{cloverleaf.eps}-S''. From now on I'll save time in the main text by referring to these combinations as ``\textbf{Command-X}'' (or whatever the relevant letter is). \subsection*{Menu shortcuts} \index{shortcuts!menu shortcuts} Firstly I have to warn you that these usually only work on PCs. Menu shortcuts are another kind of shortcut that allows you to access the program's menus without lifting your hands from the keyboard. Perhaps you've wondered why certain letters in the menu headings are underlined: for example the `F' in ``File''. If you hold down the Option key (``ALT'' on the PC, ``alt'' on most Macs), plus the letter which is \emph{underlined} in the label for the menu you want, that menu will drop down. If you continue to hold down the \textbf{Option} key you can select an option from that menu by pressing the letter underlined in its corresponding caption. With this technique and the other shortcuts it's possible to use Word quite productively without needing the mouse. \subsection*{Function key shortcuts} \index{shortcuts!function key shortcuts} The function keys, \fbox{F1}, \fbox{F2}, \fbox{F3} and so on, are at the top of some keyboards. I'm not going to discuss these in any depth. There's no meaningful labelling or logic to their functions. To me, the effort of remembering the relevant commands outweighs the energy saved by using them. Experienced users of WordPerfect have learned an array of function key shortcuts for everyday tasks. Once learned, however, these can make users of that program extremely productive. You can still make WordPerfect types nervous, however, by stealing the free keyboard overlay that tells them where the commands are. \section*{Learn the principles}\addcontentsline{toc}{section}{Learn the principles} I am a little wary of forcing too many of these tricks on you. They are a matter of personal tastes and needs. One user's essential toy is another's dusty Space-Hopper in the attic. Worse, you can waste a lot of energy trying to memorize them. The effort might be better spent on noting down a few of your favourite shortcuts. You can then keep them by your keyboard like a WordPerfect user. Any shortcuts that you can't fit onto a postcard are probably not worth the hassle of learning. \subsubsection{shortcut list} \index{shortcuts!Word's shortcut help} To find a list of shortcuts from within Word itself choose: \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} version 5} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item \textbf{? $\mid$ Microsoft Word Help $\mid$ Keyboard Shortcuts} \end{itemize} \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} version 6} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item \textbf{MS Word Help $\mid$ Reference Information $\mid$ Keyboard} \end{itemize} \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Win\\ \includegraphics[width=1.0cm]{winlogo.eps} version 6-} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item \textbf{Help $\mid$ Search for Help on $\mid$ Shortcut Keys, lists of $\mid$ Go to\ldots} \end{itemize} \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Win\\ \includegraphics[width=1.0cm]{winlogo.eps} version 7-} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item \textbf{Help $\mid$ Shortcut Keys $\mid$ Shortcut Keys} \end{itemize} \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection{``Undo'' shortcut} \index{\textbf{Undo}!\textbf{Undo} shortcut} \begin{sffamily} It's more useful to learn the general methods common to most shortcuts---together with a few ``key-combination'' techniques. This chapter is nearly all practical. Try out the basic stuff here and it will help you to get the job done. As you work through these exercises remember the most important command key shortcut of all---the \index{\textbf{Undo}!\textbf{Undo} command}``undo'' command---\textbf{Command-Z} (CTRL-Z or \includegraphics[width=0.3cm]{cloverleaf.eps}-Z). This undoes the last command you performed and can be used repeatedly to recover from a series of mistakes. (Its ``opposite'' is \index{\textbf{Redo}!\textbf{Redo} shortcut}\textbf{Command-Y}, \index{\textbf{Redo}!\textbf{Redo} command}``redo'') \end{sffamily} \section*{TRY\ldots COMMAND KEY SHORTCUTS.}\addcontentsline{toc}{section}{\textit{Try command key shortcuts}} \index{shortcuts!command key shortcuts} \begin{sffamily} First you'll experiment with using the arrow keys and the cursor movement keys to zoom around a document. On a full keyboard the cursor movement keys are between the main qwerty block on the left and the numeric keypad on the right. (If you don't have these ``special keys'' on your Mac keyboard use the alternative combinations I suggest in the notes at the end.) You'll begin by travelling to the end of the document ``LIFE'' and use the \index{\textbf{Find} command!using}\index{Find!finding text in a document}\index{search!for text}\textbf{Find} command to locate the word ``Allobrogasvexassent'' by searching backwards through ``LIFE'': \label{UsingTheFindCommand} \begin{itemize} \item Open ``LIFE''. \end{itemize} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} } \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Use \textbf{Command-End} to move to the end of the document (that's \includegraphics[width=0.3cm]{cloverleaf.eps}-End). \end{itemize} The End key might be labelled with an arrow like this: ``$\searrow$''. If you don't have an extended keypad you can use \includegraphics[width=0.3cm]{cloverleaf.eps}-3 (using the '3' on the numeric keypad, not the main (qwerty) keyboard. \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Win\\ \includegraphics[width=1.0cm]{winlogo.eps} version 6-} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Use \textbf{Command-End} to move to the end of the document \end{itemize} (That's \textbf{CTRL-End}). \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection{``Find'' shortcut} (You probably already know that you can move to the end of a line with the \textbf{End} key just as you can return to the beginning of a line with the \textbf{Home} key. You can think of \textbf{Command} as an ``amplifier'' increasing the size of the effect of any instruction you combine it with.) \begin{itemize} \item Key \textbf{Command-F}. \item Type the first few letters of the target word, say ``Allobrogas'', into the \textbf{Find What} window. \end{itemize} You don't need to match the entire text you're looking for to locate your target as long as you give the \textbf{Find} command enough letters to restrict the search. \begin{itemize} \item Below that you can choose \textbf{Up} from the \textbf{Search} drop-down box. \end{itemize} This means that you are going to look back towards the start of the document for our search term. The other options are to search \textbf{Down} (the default) and \textbf{All} through the document. \begin{itemize} \item And click in the \textbf{Match Case} check-box. \end{itemize} This will help to narrow down our search by requiring the program to match both the letters of the word and their case---UPPER or lower. \begin{itemize} \item Hit the ``ENTER'' or ``RETURN'' key (often labelled \fbox{$\hookleftarrow$}) and close the \textbf{Find} window when you arrive at the right point. \end{itemize} You have been transported to the word ``Allobrogasvexassent'' in the text. \begin{itemize} \item Click the cursor at the end of the word so you are firmly back in the editing window. \end{itemize} Say you want to move through the next few words to the word ``insolenter''. You don't need to leave the keyboard for the mouse, you don't need to hold down the right arrow key until you get RSI. Instead you can step through the text briskly, a word at a time, by holding down the \textbf{Command} key too. This works for all the so-called ``cursor keys''. \textbf{Command-\fbox{$\rightarrow$}} moves you forward on entire word, \textbf{Command-\fbox{$\leftarrow$}} moves you backward a word and combining \textbf{Command} with the up and down arrows allows us to take whole-paragraph strides through our document. \end{sffamily} \section*{TRY\ldots MOUSE SHORTCUTS.}\addcontentsline{toc}{section}{\textit{Try mouse shortcuts}} \index{shortcuts!mouse shortcuts} \index{mouse!mouse shortcuts} \index{moving!around the text} \begin{sffamily} You can start by moving the cursor around the screen with the mouse to see how it changes. \begin{itemize} \item Use the mouse to move around in the centre of a block of normal text. \end{itemize} \index{cursor!cursor shapes}\index{highlighting!document elements} \index{selecting!document elements}\index{select!how to select text}You should see the normal typesetter's \index{``I-bar''}``I-bar'' cursor. When you single-click into the text, the ``insertion point''---a black, vertical, flashing, sans-serif bar---appears at the nearest position between two letters. Anything you type will then appear to the left of the insertion point. This is the normal editing behaviour. \index{highlighting document elements!highlighting a word} \index{select!selecting a word} \begin{itemize} \item Try double-clicking. \end{itemize} Now you find that the nearest whole word is highlighted. This very handy for replacing a whole word in one go. \index{highlighting document elements!highlighting a line} \index{select!selecting a line} \begin{itemize} \item Now move the cursor slowly to the left margin of the main text. \end{itemize} Notice how it becomes an arrow-shaped pointer. \begin{itemize} \item Single-click \end{itemize} The nearest whole line is selected. \index{select!selecting a paragraph} \index{highlighting document elements!highlighting a paragraph} \begin{itemize} \item Double-click. \end{itemize} The whole nearest paragraph is selected. This is especially useful for paragraph formatting. Imagine you have devised a suitable style for diagram captions. You can go through your work just double-clicking to the left of the captions and pull down your ``caption'' \textbf{Paragraph Style} from the \textbf{Style} Combo Box to format them all. \subsubsection{moving chunks} \index{shuffle!how to shuffle text} \index{paragraphs!moving} \label{MovingAChunk}Once selected, such ``chunks'' can be moved as units. I also find this very handy for those occasions when I feel I've presented an argument in the wrong order and want to swap two paragraphs. If you've been taking a ruthlessly structured approach to writing it shouldn't be a big deal to shuffle blocks of your work in this way. \end{sffamily} \begin{sffamily} \section*{TRY\ldots MOUSE SHORTCUTS FOR TEXT-SHUFFLING.}\addcontentsline{toc}{section}{\textit{Try mouse shortcuts}} \index{shortcuts!mouse shortcuts} \index{paragraphs!how to move} \index{paragraphs!how to swap} Now you can swap the two first paragraphs of ``Life, The Universe and Everything'' using this ``whole paragraph selection'' technique. You must have \textbf{Drag-and-drop text editing} checked in the \textbf{Tool $\mid$ Options $\mid$ Edit} window before you attempt the following. \begin{itemize} \item Double-click the margin next to the first paragraph to highlight it \end{itemize} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} } \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Pick up the paragraph with the mouse. \end{itemize} \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Win\\ \includegraphics[width=1.0cm]{winlogo.eps} } \begin{sffamily} \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Pick up the paragraph by holding down the left mouse key. \end{itemize} \noindent \rule{\linewidth}{1pt} \end{sffamily} As you move the mouse you will notice that the insertion point is accompanied by a little shadow box representing the block of text. You can now drop the shadow box by releasing the mouse button almost wherever you choose. If you can't place the cutting in a particular place you will be warned by Word; the shadow box will turn into a ``no-entry'' sign. \begin{itemize} \item Move the ``shadow box'' of paragraph two above the ``real'' paragraph one. \end{itemize} You will later discover that you can also move vertical blocks of text. This can be especially useful when preparing multiple molecular sequence alignments for publication (see ``Editing sequences'', page \pageref{EditingSequences}). \end{sffamily} \begin{sffamily} \section*{TRY\ldots MIXING SHORTCUTS}\addcontentsline{toc}{section}{\textit{Try mixing shortcuts}} \index{shortcuts!combining shortcuts} This is where grasping principles, rather than memorizing facts, becomes so useful. Investigate how you can combine the above techniques to achieve even more impressive little tricks. For example, Find the ``Allobrogas'' part of ``Allobrogasvexassent'' and highlight \emph{just} that part of the word. Then notice how, if you hold down the SHIFT key while you right-arrow to the end of the word, the highlighting is \emph{extended} to the end of the word. Even fancier, you can continue extending the highlighting through the text a whole word at a time---if you have a free finger available to hold down the \textbf{Command} key simultaneously. \end{sffamily} \section*{TRY\ldots SOME FILE MANAGEMENT SHORTCUTS}\addcontentsline{toc}{section}{\textit{Try file management shortcuts}} \index{shortcuts!file management shortcuts} \begin{sffamily} \begin{itemize} \item \textbf{Close} the document you are working on first. \end{itemize} \noindent PC users can do this using a menu shortcut. \end{sffamily} \subsubsection*{Win\\ \includegraphics[width=1.0cm]{winlogo.eps} } \noindent \rule{\linewidth}{1pt} \begin{sffamily} \begin{itemize} \item Without using the mouse choose \textbf{File $\mid$ Close}. \end{itemize} \noindent If you've forgotten, you can do this by holding down the \textbf{Option} key (labelled `Alt' on a PC) together with the `F' key (for the underlined `F' in \textbf{File}) to bring down the File menu. Then, keeping the \textbf{Option} key down, choose \textbf{Close} by keying the letter `C'. (Note: the underlined \textbf{Command} letter of a menu item is not always the first letter of the word.) \end{sffamily} \noindent \rule{\linewidth}{1pt} \begin{sffamily} \noindent Next, you'll open the ``DEATH'' document using a normal keyboard shortcut. \begin{itemize} \item Type \textbf{Command-O} and \textbf{Open} ``DEATH''. \end{itemize} \noindent Now, by using the relevant shortcuts\ldots \begin{itemize} \item \ldots save the file again as though it had been modified and \textbf{Exit} without leaving the keyboard.\footnote{Hint: you can use a keyboard shortcut to save the document. PC users can combine two menu shortcuts to exit, Mac users can use a Command key shortcut: \includegraphics[width=0.3cm]{cloverleaf.eps}-Q.} \end{itemize} \begin{tabular}{llll} \includegraphics[width=0.50cm]{maclogo.eps} & \includegraphics[width=0.66cm]{winlogo.eps} & function & mnemonic\\[1.0ex] \includegraphics[width=0.3cm]{cloverleaf.eps}-O & CTRL-O & ``\textbf{Open} a document'' & \textbf{O}\textit{pen document}\\ \includegraphics[width=0.3cm]{cloverleaf.eps}-S & CTRL-S & ``\textbf{Save} the current document'' & \textbf{S}\textit{ave document}\\ \includegraphics[width=0.3cm]{cloverleaf.eps}-N & CTRL-N & ``\textbf{Open} a new document'' & \textbf{N}\textit{ew document}\\ \includegraphics[width=0.3cm]{cloverleaf.eps}-P & CTRL-P & ``\textbf{Print} current document'' & \textbf{P}\textit{rint document}\\ \end{tabular} \end{sffamily} \section*{TRY\ldots SOME CUTTING-AND-PASTING SHORTCUTS}\addcontentsline{toc}{section}{\textit{Try cutting-and-pasting shortcuts}} \index{shortcuts!for cutting-and-pasting} \begin{sffamily} Staying on the keyboard, find the word ``Kilburn'' again, cut it out and paste it at the head of the next paragraph (the one beginning ``Caesari renuntiatur'')\ldots \begin{tabular}{llll} \includegraphics[width=0.50cm]{maclogo.eps} & \includegraphics[width=0.66cm]{winlogo.eps} & function & mnemonic\\[1.0ex] \includegraphics[width=0.3cm]{cloverleaf.eps}-C & CTRL-C & ``\textbf{Copy} current selection'' & \textbf{C}\textit{opy selected}\\ \includegraphics[width=0.3cm]{cloverleaf.eps}-X & CTRL-X & ``\textbf{Cut} current selection'' & \textbf{E}\textit{xtract selected}\\ \includegraphics[width=0.3cm]{cloverleaf.eps}-V & CTRL-V & ``\textbf{Paste} current selection'' & \textit{Retrie}\textbf{V}\textit{e selected}\\ \end{tabular} \end{sffamily} \section*{TRY\ldots SOME MARKUP SHORTCUTS}\addcontentsline{toc}{section}{\textit{Try markup shortcuts}} \index{shortcuts!mark-up shortcuts} \begin{sffamily} \ldots and reformat it (the word ``Kilburn'') as a level 1 heading. Note that these mark-up shortcuts don't work under Mac Word 5. \begin{tabular}{llll} \includegraphics[width=0.50cm]{maclogo.eps} & \includegraphics[width=0.66cm]{winlogo.eps} & function & mnemonic\\[1.0ex] \includegraphics[width=0.3cm]{cloverleaf.eps}-OPTION-1 & ALT-CTRL-1 & ``apply \textbf{Heading 1} style'' & \textit{Heading} \textbf{1}\\ \includegraphics[width=0.3cm]{cloverleaf.eps}-OPTION-2 & ALT-CTRL-2 & ``apply \textbf{Heading 2} style'' & \textit{Heading} \textbf{2}\\ \includegraphics[width=0.3cm]{cloverleaf.eps}-OPTION-3 & ALT-CTRL-3 & ``apply \textbf{Heading 3} style'' & \textit{Heading} \textbf{3}\\ \includegraphics[width=0.3cm]{cloverleaf.eps}-SHIFT-N & ALT-CTRL-N & ``apply the \textbf{Normal} style'' & \textbf{N}\textit{ormal}\\ \end{tabular} \\ \end{sffamily} \noindent \rule{\linewidth}{1pt} \subsection*{Autotext and Macros} \index{\textbf{Autotext}\index{Macros}} \begin{sffamily} \noindent \rule{\linewidth}{1pt} \textbf{Note: don't try the following under Mac Word 5.} \noindent \rule{\linewidth}{1pt} \index{phrases!frequently used!automating}You will, of course, get bored with typing ``\textit{Salmonella typhinurium}'' one hundred and seventy three times, even in the abbreviated form. \index{\textbf{Autotext}!setting up}\textbf{Autotext} is the simple answer to this problem. Not only does it allow you to insert words without typing them in full, it has the added advantage that they will be made to appear in the correct format---in this case italicised. You could attach any style to the letters of your own words and phrases. The idea is that Word maintains a small dictionary of frequently used words or phrases which it recognises as you type. In earlier versions of the program you type the first few letters of the word and click the \textbf{Autotext} button on the toolbar and Word completes your text automatically. Try it with the phrase ``\textit{T. Labienum}''. \end{sffamily} \section*{TRY\ldots SETTING UP AN AUTOTEXT PHRASE}\addcontentsline{toc}{section}{\textit{Try setting up an autotext phrase}} \begin{sffamily} \begin{itemize} \item In the document ``LIFE'' highlight the phrase ``\textit{T. Labienum}''. \end{itemize} See ``Navigation Shortcuts'' above for how to use the \textbf{Find} command to locate it. \begin{itemize} \item Press \textbf{Command-I} to put the phrase in italics. \end{itemize} For demonstration purposes you will put it in italics as though that was how you always wanted the phrase to appear. \begin{itemize} \item Now click on the \textbf{Autotext} button \end{itemize} This looks like a hand pointing onto a keyboard. If you don't have one on your \textbf{Standard} toolbar you may have to jump ahead to the next section (``Custom toolbars'', page \pageref{CreateACustomToolbar}) to figure out how to add one. \begin{itemize} \item Once you've clicked \textbf{OK}\ldots \end{itemize} \ldots the phrase has been added to the \textbf{Autotext} dictionary. \begin{itemize} \item Now start a new paragraph and begin typing ``T. La'' \end{itemize} Under Word 95 or later the complete phrase should pop up in a tiny window next to the cursor automatically and you can just hit the ``ENTER'' or ``RETURN'' key (often labelled \fbox{$\hookleftarrow$}) to have the phrase finished off in the correct format. Earlier versions of the program require you to click the \textbf{Autotext} button again to do the job. \end{sffamily} \noindent \rule{\linewidth}{1pt} \section*{TRY\ldots ADDING A TOOLBAR BUTTON.}\addcontentsline{toc}{section}{\textit{Try adding a toolbar button}} \index{toobar!custom} \index{customizing!toolbars} \subsection*{Custom toolbars} \index{custom toolbars} \begin{sffamily} \label{CreateACustomToolbar} You work may lead you to use certain commands more frequently than the average user. It can help if the ones you use most commonly are gathered on the toolbars so you can be access them with a mouse-click. If you are a reasonably fluent typist you may well find it's quicker to learn the keyboard shortcuts. If you do want to use buttons, Word makes it very simple to place your favourites at hand. \end{sffamily} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} version 5 } \begin{sffamily} \noindent \rule{\linewidth}{1pt} Version 5 of Word for the Mac seems only to allow you to add a new button by \emph{replacing} an existing one. If you really want to do this\ldots \begin{itemize} \item \ldots \index{toolbar!customize!Mac 5}click on the \fbox{$\bigtriangledown$} button on the main toolbar and choose \textbf{Customize}. \end{itemize} \noindent The instructions for changing a toolbar button are displayed in a pane in the window that then appears. \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} version 6- } \noindent \rule{\linewidth}{1pt} \begin{sffamily} For the Mac version you'll add as an example a \textbf{Document Find} button \begin{itemize} \item \index{toolbar!customize!Mac 6-}Choose \textbf{Tools $\mid$ Customize}. \item Select the \textbf{Toolbars} tab \item Highlight \textbf{File} in the left hand \textbf{Categories} pane \item Click on the image of binoculars on top of a folder \end{itemize} In the \textbf{Description} box the text ``\textbf{Locates documents\ldots}'' will appear. \begin{itemize} \item Drag this button to whichever toolbar you'd like it to appear on. \item Click \textbf{Close} \end{itemize} Your new \textbf{Document Find} button should now be ready for use. \begin{itemize} \item Try it out. \end{itemize} \end{sffamily} \noindent \rule{\linewidth}{1pt} \subsubsection*{Win\\ \includegraphics[width=1.0cm]{winlogo.eps} version 6-} \noindent \rule{\linewidth}{1pt} \begin{sffamily} \begin{itemize} \item \index{toolbar!customize!Win 6-}Choose \textbf{Tools $\mid$ Customize}. \end{itemize} You should now see the \textbf{Customize} window with the \textbf{Commands} tab selected. \begin{itemize} \item If necessary select the \textbf{Commands} tab. \item If you are reading this to find out how to insert a missing \textbf{Autotext} button on your toolbar, choose \textbf{Edit} or \textbf{Insert} in the left-hand pane and the \textbf{Autotext} icon, a hand pointing at a keyboard, in the right. Otherwise select \textbf{File} in the \textbf{Categories} pane on the left of the window and find the\textbf{Print Setup} icon, a page with four ruled margins, in the right-hand pane. \end{itemize} Pick it up with the left mouse button and drop it between a couple of other icons on the \textbf{Standard} toolbar. Once you've exited from the \textbf{Customize} window you can use the button just like any other. \noindent \rule{\linewidth}{1pt} \end{sffamily} \chapter{Grammar and prose style} \index{grammar} \index{style!prose style} ``Keep It Simple Stupid'' is a great geek motto. It does what it says. Such a simple saying is easy to remember and easy to understand. It also makes sense in many kinds of work outside computing. Do not be seduced into thinking that you should produce obscure, \index{jargon}jargon-ridden prose because other ``more successful'' scientists do so. Even first-rank journals like \textit{Nature} and \textit{Science} have allowed crimes against English to be committed in their pages. \index{\textit{Nature}}\textit{Nature} is a good place to start, however, if you want an example of elegant scientific writing. One of the most cited papers of all time, \index{Crick!and Watson}Crick and \index{Watson!and Crick}Watson's original description of their double-helical model of DNA structure, is a masterpiece of scientific exposition. It can be found in the original 1953 \textit{Nature}, volume 171, page 737 or on the Web at \textit{Nature}'s Web site, \texttt{www.nature.com}, as well as in various anthologies. This book is about using tools to finish your writing so I won't whitter on too much about the niceties of language. I will mention a few simple and important things to consider when producing your masterwork. I will also recommend two short readings that might turn out to be as important to your writing as your word-processor. Finally I will describe some crude, but not entirely useless, facilities provided by Word to check your writing. \section*{Writing well}\addcontentsline{toc}{section}{Writing well} \index{writing!writing well} \subsection*{Jargon} \index{jargon} Jargon is more easily excused in science. Even in science, remember that there are two---and only two---reasons to resort to its use: \paragraph{To describe entirely novel phenomena} for which there is no existing vocabulary. There is, for example, no alternative to labelling such a cell a ``B-lymphocyte''. \paragraph{As shorthand.} ``Major Histocompatibility Complex'' is not only boring to write fifty times, it's pretty boring to read. You don't need me to tell you that it makes sense to use ``MHC''. \subsection*{Voice} \index{voice!which voice to write in} This seems like a little thing, but spawns big arguments. Science is supposed to be an objective, collective activity. In research ``things get done'' in real life ``someone does things''. School chemistry teachers may well have encouraged you to write ``a blue colour was observed''. Unfortunately the use of the passive voice is generally considered weak writing. My advice is simple, but you may be instructed by others to ignore it. If so, listen to them, not me. In preference I believe you should write: ``we observed a blue colour'', or, since a thesis is supposed to be solely your own work: ``I observed a blue colour''. \subsection*{Filler} \index{filler!why it isn't big or clever} No supervisor will argue with my related advice on horrible filler phrases. These are favourites of those who desperately want to pack space or sound impressive. Why use ``lend support to'' when ``support'' will do fine? Why say ``the fact that'' to introduce a sentence when often ``Since'' serves the same purpose. Don't try to impress people, try to inform them. Part of this problem derives from habitual use of the passive: ``these results are representative of'', rather than ``these results represent''. \subsection*{Ambiguity} \index{ambiguity} Another possible reason for such woolly language is that it avoids making too strong a statement of fact or belief. Scientific reasoning, especially in biology, is often about the judicious weighing of relative probabilities. It is good science to doubt results and conclusions. When you are doubtful say so. When you are not don't hedge. One of the strengths of English as a literary language is its endless potential for rendering shades of meaning. A writer of literature can use this potential to offer readers' imaginations many different pictures of the same scene. A writer of science should use it to describe events with precision and clarity. \index{ambiguity!kills (frequent-fliers)}Ambiguity is fine for novelists, but much less desirable in other occupations: air-traffic control, say. \subsection*{Stacked nouns} \index{stacked nouns!hurt like stacked heels} \index{nouns!stacked} In recent years this horrible phenomenon has grown in prevalence to the point when practically every title in Nature is a string of stacked nouns, for example ``Time-reversal symmetry-breaking superconductivity in $\mathrm{Sr_2RuO_4}$''. Try not to do it, or at least keep it under control. There's nothing worse than driving away your readers before they've even started reading your text. \subsection*{Read the instructions} Find out how your paper (notes to authors) or thesis (university statutes) is supposed to be constructed and printed and how long it's supposed to be. Then follow the stipulations to the letter. I've seen first hand what happens at the editorial end and you won't be thanked for not following simple instructions. There's a lot more room in that wastepaper basket then there is in an edition of a good journal. \subsection*{Foreign or classical words or phrases} \index{foreign!foreign words or phrases} \index{classical!classical words or phrases} \textit{Nein}, \textit{non}, no. Some Latin words are useful and accepted parts of written English, \textit{e.g.} \textit{via}, \textit{etcetera}. For those, English alternatives actually sound a little strange, though it's nice if you take the trouble to italicise the Latin. Others are just pretentious and annoy the people whose language you are abusing. I had a German physiologist friend who exploded every time she heard the word ``\textit{Zeitgeist}'' being misapplied by some media commentator. Even some of the common Latin abbreviations have better alternatives---I always prefer ``that is'' to \textit{i.e.}. If you think this is a strange suggestion, remember people were using ``\textit{vide supra}'' for ``see above'' not so long ago. Why? I would go further still and suggest you follow George \index{Orwell! George}Orwell's excellent advice (see ``Recommended reading'' below) to choose words with Anglo-Saxon roots over those of Latin derivation at every opportunity; ``make up'' rather than ``formulate'' your buffers. \subsection*{Write sentences} \index{sentences} The previous paragraph breaks this rule repeatedly for effect. The only effect you wish to have on your scientific readership is to make them understand and believe your work. People are used to sentences. If you manage at least to string together a noun, a verb and an object a few times in a row there will be something of meaning for your audience to take from your work. If you don't know what nouns and verbs are, visit UCL's free on-line grammar tutor at: \index{internet grammar} \begin{quotation} \begin{verbatim} http://www.ucl.ac.uk/internet-grammar/ \end{verbatim} \end{quotation} It helps if you keep those sentences short and free of convolutions, too. This is especially important if your technical terms are long. \subsection*{Write paragraphs} \index{paragraphs} This is an extension of my original argument that all writing should be done from the level of the global structure ``downwards'' to the level of the individual words. A paragraph should be able to stand alone and convey a single step in your argument. Some divisions in a paper are defined by the specifications of the work, the division of your argument or report into distinct blocks of thought is up to you. Give your reader time to pause and think over what you have written. If nothing else, remember that good skim-readers (scientists?) find most of the information worth retaining in the first and last sentence of each paragraph. \section*{Tools for good writing}\addcontentsline{toc}{section}{Tools for good writing} \subsection*{Use a dictionary} \index{dictionary!choosing non-virtual} Spell-checkers will only take you so far (see below). Not only will a dictionary help you to ensure you have the right word spelt correctly, a good one will warn you of common errors, help you to find the past participle of a verb or the correct adjective derived from a noun. It might also give you something to read when you are fed up with your work. (The \textit{Oxford Shorter} is almost as entertaining as the full \textit{Oxford English Dictionary} and much more conveniently sized---unless compared with the CD-ROM version.) If English is your second language you probably never go near a word-processor without a dictionary anyway. \subsection*{Recommended reading} \index{reading!recommended reading} I am going to suggest two short sources because, if you are reading this book, you probably don't have time for a leisurely stroll through a longer, but more complete work. \subsubsection*{Orwell} George Orwell's \textit{Politics and the English Language} is possibly the greatest essay on the use of modern English ever composed, regardless of its original intended audience. It also has the advantage of being much shorter than \textit{Fowler's English Usage}. If you just want to read it just search the Web for its title (as a phrase) and you will be directed to one of many freely-available transcripts. It is also available on dead tree in \textit{Inside the whale and other essays}, published by Penguin, ISBN 0140182322. \subsubsection*{Strunk} \index{Strunk!Jr., William} \index{style!\textit{Elements of Style}} Strunk's \textit{The Elements of Style} is also available on the Web (from Columbia University's on-line library), but is far more practical in book form: \begin{quotation} Strunk, White, \textit{The Elements of Style}, published by Prentice-Hall, ISBN 0205191584 \end{quotation} I first read this while waiting for an interview. It made such an impression on me that it even changed the way I spoke. It's also short and cheap. \section*{Word's writing tools}\addcontentsline{toc}{section}{Word's writing tools} \index{tools!Word's writing tools} Word comes with its own ``proof reader''; the program's built-in tools can handle those boring editing chores: word-counting, spell-checking and, in later versions, grammar-checking. In more recent versions (Word 7.0/95 onwards), Microsoft played catch-up with other word-processors like WordPerfect by adding ``while-you-type'' correction of mistakes. This became the default. If you run Word straight out of the box, errors in spelling and grammar underline themselves in red and green respectively as you worked. Check page \pageref{SetUpOptions} for advice on how to set these up or turn them off for scientific writing. \subsection*{Spelling and Grammar} \index{\textbf{Spelling and Grammar}} Once you have adjusted these facilities according to your tastes or my advice, there are a couple of things to be wary of. Firstly, it's possible to misspell the word you want to write while spelling another word perfectly correctly. My own Word spell-checker is completely harpy wit this sentence four example. Secondly, if you are foolish enough to have the grammar-checker running continuously, you can safely ignore about eighty percent of its judgements on your work simply because it has none---judgement, that is. The grammar-checker simply looks for what it categorises as doubtful patterns of language components; it has a superficial ``grasp'' of syntax and style, but no understanding of semantics, that is, the meaning of what you have written. It is, however, useful in drawing your attention to long sentences. \subsection*{Word Count} \index{\textbf{Word Count}} This is particularly handy when you are working to an institution's, editor's or supervisor's specifications and far more accurate than your counting individual words or making an estimate on the basis of line length. It's also quite satisifying to watch the number of words you have written grow as you work. \section*{TRY\ldots SOME WRITING TOOLS}\addcontentsline{toc}{section}{\textit{Try some writing tools}} \index{tools!Word's writing tools!how to use them} \begin{sffamily} If you have followed this book so far these should be trivial commands for you to master. \subsubsection{word count} \index{\textbf{Word Count}} To count all the words in your document, making sure that none of the text is highlighted\ldots \begin{itemize} \item Select \textbf{Tools $\mid$ Word Count} \end{itemize} \end{sffamily} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} version 5} \noindent \rule{\linewidth}{1pt} \begin{sffamily} \ldots on Mac Word v5 you then need to\ldots \begin{itemize} \item Click \textbf{Count} \end{itemize} \noindent \rule{\linewidth}{1pt} \end{sffamily} \begin{sffamily} You can restrict the count by highlighting the relevant portion of the text first and running \textbf{Word Count} on that section only. (This is good for, say, excluding bibliographies.) \end{sffamily} \subsubsection*{Win\\ \includegraphics[width=1.0cm]{winlogo.eps} version 6-} \noindent \rule{\linewidth}{1pt} \begin{sffamily} The other way to obtain these on a PC running 95 or a later version is to\ldots \begin{itemize} \item Choose \textbf{File $\mid$ Properties} and click on the \textbf{Statistics} tab. \end{itemize} \end{sffamily} \noindent \rule{\linewidth}{1pt} \subsubsection{Spell Check} \index{\textbf{Spell Check}} \begin{sffamily} To begin a spell check downwards through your work from your current position: \begin{itemize} \item Select \textbf{Tools $\mid$ Spelling} (on some PC versions you can just hit \fbox{F7}) \end{itemize} If you just want to check the spelling of a single word, highlight that word first before you run the spell-checker. \subsubsection{Thesaurus} \index{\textbf{Thesaurus}} Also useful, when you are stuck for a word, is the facility to call up a menu of alternative words from the \textbf{Thesaurus}: \begin{itemize} \item Highlight the word and choose \textbf{Tools $\mid$ Thesaurus}. \end{itemize} \subsubsection{Grammar} \index{\textbf{Grammar}} You can also use this method to access \textbf{Tools $\mid$ Grammar} and so on\ldots \end{sffamily} \chapter{Fonts, special characters, and equations} \index{fonts!general} \section*{Meditations on typesetting}\addcontentsline{toc}{section}{Meditations on typesetting} \index{typesetting} Most people use one of Word's proportional fonts for the bulk of their typing. This produces a slicker output, but anyone who has used professional typesetting tools will realise that the results don't really compare with those from a proper publishing outfit. Word makes this task easier by cutting corners. Here are some of the little problems this causes and some ways around them. \subsection*{Fonts: fixed and proportional} \index{fonts!fixed \textit{vs}. proportional} If you look at a pre-80s thesis, chances are it will have been typed up by some long-haired student's kindly landlady on an old Smith-Corona. The typescript, probably something like Courier, is said to be ``fixed''; every character is exactly the same width, even the letter `i'. Then, this made it easier, for example, to line up tables of results---columns of text and figures could be made to line up vertically on the page with the minimum of fuss about ``decimal tabs'' and the like. Of course a certain amount of pre-planning was essential and the results could be ugly. \index{WYSIWIG}Since the advent of desktop publishing and so-called WYSIWYG (``What You See Is What You Get'') editors, proportional fonts are the thing. That ``thing'' is usually Times New Roman or Palatino. Not only are the horizontal widths of the individual characters governed by their shapes, but the width of two anagrams (words with the same letters in a different order) may well vary because of phenomena such as ``kerning''---where certain combinations of letters are moved closer so they fit tidily and don't blot at the points where they overtype. Look at the dot of the `i' in ``fit'', for an example. Word does most of this automatically, but nowhere near as elegantly, as a proper typesetting program like ``\TeX''. The only reason I mention this phenomenon here is because it is quite important to be aware of it when performing other tasks (for example, see ``Editing sequences'', page \pageref{EditingSequences}). Experiment with the fonts available on your machine, for example by comparing the lengths of equal numbers of `W's and `I's, and make a note of which fonts are fixed so you can identify them when you need to. \subsection*{Ellipsis} \index{ellipsis} Similarly there may be a difference between three successive full-stops, ``...'', and an ellipsis, ``\ldots''. This difference varies from font to font. In Word 95, \linebreak \index{\textbf{AutoCorrect}!and ellipsis} the built-in \textbf{AutoCorrect} feature should automatically insert an ellipsis for three dots as you type---provided you've remembered to switched it on. \subsection*{Hyphens} \index{hyphens} There is a less nit-picking distinction to be made between a hyphen, as you might find in the name of Mr Cholmley-Warner, the \index{dash!``en-dash''} ``en-dash'' you use to identify the years he was alive (1900--1983) and the \index{dash!``em-dash''}``em-dash'' you might---pay attention now---use for the sort of parenthetical comment he would make during one of his public service broadcasts. An em-dash is longer than a hyphen or \index{dash!en-dash}``en-dash'', in same way a proportionately-spaced `m' is longer than a proportionately-spaced `n'. Word prefers to break words across lines at hyphens, while em-dashes and en-dashes are, if possible ``elasticated'' to the words around them. I like to think the difference matters; now you know enough to make your own choice. I must warn you that Windows 3.11 (and earlier) has problems with all kinds of hyphens so don't even think about these considerations if that is the operating system on your machine. \subsection*{Full justification} \index{justification!of text} Full justification blocks both the left and right sides of a chunk of text against their respective margins. When producing text arranged in columns it is essential, though columnar text should really be set with a proper typesetting program rather than Word for reasons I am about to describe. When the text is set to one side to provide a margin for notes and icons, full justification can greatly improve the overall appearance of a ``designed'' document. I never use this setting for academic writing, however. Instead I always leaving the main body of my work ``ragged right''. The reason is simple: in this respect Word once again is only so smart about handling unusual sentences. Occasionally a sequence of words of strange lengths (as often arises in a academic work) can become so widely spaced-out that the text becomes hard to read. Often while you are working with a fully justified page (and especially as you approach a section break) you will find the words of the paragraph you are currently typing wandering in a very distracting way. This is because Word is calculating their correct distribution of the text across the page on-the-fly. Not nice. If you really do want your text to appear like this you may find it easier to work on left-justified text and justify the right column immediately before printing out. If you have followed my advice on document structure you can fully justify all the \textbf{Normal} text without affecting titles and headings. \subsection*{Styles without content} \index{styles!reformatting fonts as} \label{StylesWithoutContent} This trick (drawn to my attention by Gillian Hynes) allows you to make a global change from an arbitrary font style you may have used for secondary level headings, say. If you weren't a good boy/girl and failed to mark up the first draft of your thesis by content then the first thing you do after reading this guide is devote half-an-hour to doing so. The following exercise shows how to do it with the sample document, DEATH. If you have Word version 5 for Mac, your next job is to get hold of a newer version of the program as the following won't work for you. \section*{TRY\ldots REPLACING A FONT WITH A STYLE}\addcontentsline{toc}{section}{\textit{Try replacing a font with a style}} \index{fonts!replacing with a style} \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} version 5} \begin{sffamily} \noindent \rule{\linewidth}{1pt} Don't try this under Mac Word 5! \noindent \rule{\linewidth}{1pt} \end{sffamily} \subsubsection*{both\\ \includegraphics[width=0.50cm]{maclogo.eps} \includegraphics[width=0.66cm]{winlogo.eps} version 6-} \noindent \rule{\linewidth}{1pt} \begin{sffamily} \begin{itemize} \item Open the original, poorly formatted version of DEATH. \item Open a \textbf{Replace} box. You can do this with \textbf{Command-H}. \end{itemize} (Remember, the \textbf{Command} key is marked \includegraphics[width=0.3cm]{cloverleaf.eps} on a Mac and ``Ctrl'' or ``CONTROL'' on a PC). You'll start by clearing the \textbf{Find What} window (where you'd normally type the text you're looking for). You are going to look for text with a particular appearance, and ignore its content. \begin{itemize} \item Click the cursor into the \textbf{Find What} field and clear any existing text there. \item Set \textbf{Search} to \textbf{All}. \item Select the drop-down box marked \textbf{Format}. On a PC you may need to to click \textbf{More} first to get the full selection of commands, including the \textbf{Format} box. Choose \textbf{Font} from the drop-down menu. \end{itemize} In the next box which pops up you can specify exactly (or inexactly) the font you are after. \begin{itemize} \item Choose \textbf{Times New Roman}, \textbf{Italic}, \textbf{14pt}. \end{itemize} After you\ldots \begin{itemize} \item \ldots \textbf{OK} this\ldots \end{itemize} \ldots you can\ldots \begin{itemize} \item \ldots click in the \textbf{Replace With} field of the \textbf{Find} box. \end{itemize} This time\ldots \begin{itemize} \item Choose \textbf{Style} from the (\textbf{Format}) drop-down menu. In this example you select \textbf{Heading 2} from the dialogue box that follows. \textbf{OK} this. \end{itemize} Now you can simply move through the document, clicking \textbf{Replace} to repair the earlier mistake. \noindent \rule{\linewidth}{1pt} \end{sffamily} \section*{Using the Equation Editor}\addcontentsline{toc}{section}{Using the Equation Editor} \index{equations!formatting} Seriously mathematical scholars don't even bother with Word. Although easier and quicker to pick up, the program can't offer the precision and power of a custom-built typesetting packages like \TeX{} or \LaTeX{}. These document preparation systems are disciplines in themselves. Complicated formulae are usually only sprinkled through biological literature, if they appear at all. You don't need to learn what are effectively programming languages to cope with these limited requirements. Word is now well-enough equipped to set occasional equations adequately. This is a brief introduction to the use of the Equation Editor. You'll need the Editor on screen to make sense of the following. Again, I will emphasise principles over details. \section*{TRY\ldots BUILDING AN EQUATION}\addcontentsline{toc}{section}{\textit{Try building an equation}} \index{equations!how to format} \index{\textbf{Equation Editor!how to use}} \begin{sffamily} \begin{itemize} \item Highlight \textbf{Object} on the \textbf{Insert} menu. \item Choose (\textbf{Microsoft}) \textbf{Equation} and click \textbf{OK}. \end{itemize} The point of insertion becomes a box surrounded by hatching and squares. Floating over the page is a new toolbar. This shows various rectangles containing example equation components. If you click on one of them---say the one showing uppercase Greek letters: \fbox{$\Lambda\Omega\Theta$}---a drop down box appears with various boxed characters. To retract the box, click on the \textbf{Equation Toolbar} background. Clicking on one of these ``sub-boxes'' will cause the corresponding character to appear in the first position in the equation frame. This is the basic method of inserting equation characters. Word will take care of the spacing once the equation is complete. In the same way, if you can use a normal upper- or lowercase letter of the English alphabet you simply type it from the keyboard and Word uses mathematical conventions to set the character appropriately relative to other elements in the equation. Of course, it's not all this simple. Often you will use a framework character, like a summation symbol, $\sum$, or a matrix grid, which has standard slots into which you want to insert other symbols. As an example you'll make a general expression of the mean, as the equation for the expected value of, a discrete random variable $E(X)$. Given that the frequency function of $x$ is $p(x)$: \begin{displaymath} E(X)=\sum_{i}x_ip(x_i) \end{displaymath} It looks pretty straightforward, but even this (relatively) well-known equation is complicated enough to introduce most of the techniques you'll use. After you have moved to a new line and invoked the equation editor, the first part of the expression is easy to render by typing in the characters as they stand straight into the ``magic box'': \begin{displaymath} E(X)= \end{displaymath} \begin{itemize} \item Without typing any spaces---for example before or after the equals sign---key in the characters above as they stand. \end{itemize} They will appear in the appropriate equation font as you type. If you did hit the spacebar you probably heard ping of disdain from your computer. You should let it take care of the spacing. Next you need to summon the summation framework. You'll notice there's a separate pull-down box for summation symbols. \begin{itemize} \item Pull down the box of summation symbols \end{itemize} There are a range of different configurations: a capital epsilon with a slot below only, one with slots above and below, one with two slots slightly forward of the symbol and so on. The one you want has one slot directly underneath. \begin{itemize} \item Select the summation symbol with a single field beneath it. \end{itemize} When you select it, the symbol itself will appear and your cursor will wait in the space immediately after it. This is the first field of this framework. Although you can move to the next field (the slot below) by pressing the tab button, \fbox{$\rightarrow\!\mid$}, \emph{don't} do that yet. \begin{itemize} \item Type in the letter `x'. \item Click on the shaded ``subscript'' template. \end{itemize} This is a shaded upright rectangle attended by two tiny boxes, one subscripted and one superscripted. If the appropriate symbol for this isn't obvious just browse the Equation Editor icons with your mouse until the right caption appears. \begin{itemize} \item In the drop-down subscript menu select the single-subscript template. \item Type a letter `i' into the tiny subscript field that appears. \item Hit the tab button to move out of the subscript area then type: \begin{displaymath} p(x \end{displaymath} \item Now use the shaded subscript template to place the next subscript letter, `i'. \item Once you have ``arrowed'' out of the second subscript field you can close your brackets and tab once more. \end{itemize} This will bring you to the field under the summation symbol where\ldots \begin{itemize} \item \ldots You can finally type in your last letter `i' subscript underneath the summation symbol. \end{itemize} If you close the \textbf{Equation Editor} you can return to the main text. The equation appears at your original insertion point as a self-contained unit which you can move within your document or re-edit by double-clicking within its frame. \end{sffamily} \section*{Editing sequences (molecular biology)}\addcontentsline{toc}{section}{Editing sequences (molecular biology)} \index{sequence!editing molecular sequences} \label{EditingSequences} The sequence alignments used by molecular biologists are exactly that:\linebreak \emph{align}ments. The proportional fonts that are the default in Word are completely unsuited to the task. The letter `I' for ``isoleucine'', say, simply doesn't occupy the same horizontal space as the letter `M' for ``methionine'' and the two could never be lined up usefully. Over the course of an entire peptide sequence such differences in length might average themselves out, but this is hardly the point. The simple answer is to use a fixed-width font like Courier---there should always be a typewriter-style font available with any installation of Word---whose letters are all the same length. Better still, you should use a style which forces all the possible components of any given paragraph to have a fixed length. For example the \textbf{Macro Text} style (unfortunately not available under Word 5 for the Mac) can be obtained by highlighting your sequence characters and choosing \textbf{Format $\mid$ Style}, selecting \textbf{List $\mid$ All Styles} in the bottom left hand drop-down box and selecting \textbf{Macro Text} from the \textbf{Styles} menu. \index{select!vertical select} \index{select!column select} This second tip was given to me by Matilda Katan who saved me hours of tedium by pointing out that entire vertical chunks of aligned sequences could be moved around just as simply as continuous horizontal blocks. Hold down the \textbf{Option} key (``Alt'' on a PC, ``alt'' on most Macs) before and while you click the mouse so you can extend a highlighted area in both dimensions. This way, for example, you can lift the last 10 columns of 10 aligned sequences and place them at the start of a following paragraph of the alignment. \chapter{EndNote and EndLink} \index{bibliography!how to make} \index{reference!management software} \index{EndNote}\index{EndLink} \section*{What is EndNote?}\addcontentsline{toc}{section}{What is EndNote?} \index{EndNote!what is EndNote} EndNote is a simple, but very useful, program that compensates for a deficiency in Word. The latest versions of Word come with a talking paperclip and an animated dog in a cape, but are yet to handle large numbers of references with the aplomb of some DOS versions of WordPerfect. So we poor-scientist Word-users often pay considerable extra sums for decent reference management. There are several such packages on the market, but I have chosen to focus on EndNote because it is commonly used by biologists. It's also very good at what it does---if overpriced. \subsection*{EndNote versions} \index{EndNote!EndNote versions} If you are using versions from release 3 onwards some of my explanations for downloading references from the Web and importing them into EndNote will be completely superfluous. These later versions connect to the Internet automatically to allow searching and collecting references from on-line databases as though they were local. My first recommendation to you, therefore, is buy EndNote 3 or later. Ultimately it will repay its silly price in saved time. EndNote comes with a hefty instruction manual or two. If you want to start using the program quickly read this chapter. If you want to exploit it fully please real the detailed instructions that came with your disks. \begin{bfseries} If you have EndNote 2 I assume you have ``EndNote Plus'' or ``EndNote'' and ``EndLink''. Where necessary you should take ``EndNote'' to mean the main package itself and all of its accessory programs. I have made no guarantees that the exercises in this book will work on your particular set-up, but this section is even more likely to be useless to you since there are so many possible combinations of machine type, EndNote version and Word version that I cannot possibly cover them all. Please let me know of your problems. \end{bfseries} \section*{How it works}\addcontentsline{toc}{section}{How it works} If you have never used a reference management program before then, once again, it's important that you grasp the basic principles before I explain the details of everyday use. \subsection*{Libraries and repetition} \index{library!EndNote libraries} Most scientific writing is specialised; your work and therefore most of your publications will tend to be about a single subject area. As a result you will find yourself citing a core of papers judged important in your field over again. Rather than cutting-and-pasting these references from publication to publication EndNote allows you to collect a library of these relevant citations and insert when you need to. \subsection*{Bibliographies and style} One drawback with simply cutting-and-pasting the same reference from one article to another is that you may well submit your work to more than one publication. Each journal has its own house style. Some may prefer authors to produce their bibliographies as lists of entries whose elements are separated by commas with the full title of the article in italics. Others may require a full-stop before the chapter and page reference and the all the elements of each reference in the same font. Inserting or modifying references to ensure that your work is formatted according to such requirements can be painfully tedious. Even worse is the difficulty of keeping track of numbered references as a paper is modified by the \index{citations!insertion of} insertion of other citations and the shuffling of the body text. EndNote saves you these problems. Once you have marked the places in the main text of your article where specified citations from your library should appear, the program generates a bibliography automatically on request using the details you have entered into your library for each reference. \subsection*{Searching Bibliographies} Of course, your well-tended library of references is a mini-database which you might want to search for information. EndNote lets you do this too. \subsection*{How to make a library} \index{library!making in EndNote} \subsubsection*{the best way} I love using computers to reduce drudgery, but the best and most straightforward way to create your EndNote library is to type the entries directly into the program. I recommend this for two reasons---one professional, one practical. Firstly, I believe you should cite the smallest number of the best papers most directly relevant to your work. \emph{These should be papers you have read}---not necessarily from start to finish in obsessive detail, but thoroughly enough to understand and assess them. You should get into the habit of updating your collection of references whenever you find something interesting. As soon as you encounter a relevant publication you should type the title, author names, source publication and so on into EndNote. The second, practical, reason for this approach is that you know that you have checked the entry yourself. If you copy someone else's reference you can't be sure they haven't made a mistake when they entered it. If you haven't read the original paper, you don't know if it is as relevant as claimed. Worse, your source may have, in turn, copied someone else's mistakes. Quite horrible citation errors have been known to propagate themselves from paper to paper in this way through the simple laziness of authors. No, even databases like Medline aren't perfect. \section*{TRY\ldots MAKING A TEST LIBRARY FOR YOURSELF}\addcontentsline{toc}{section}{\textit{Try making a test library for yourself}} \index{library!how to make in EndNote} \begin{sffamily} \begin{itemize} \item Open EndNote \end{itemize} You will be prompted for the name of a library file. You don't have one yet so: \subsubsection*{Mac\\ \includegraphics[width=0.75cm]{maclogo.eps} } \noindent \rule{\linewidth}{1pt} \begin{itemize} \item Choose \textbf{New} \end{itemize} \end{sffamily} \noindent \rule{\linewidth}{1pt} \subsubsection*{Win\\ \includegraphics[width=1.0cm]{winlogo.eps} } \noindent \rule{\linewidth}{1pt} \begin{sffamily} \begin{itemize} \item Choose \textbf{Cancel} then choose \textbf{File $\mid$ New} \end{itemize} \end{sffamily} \noindent \rule{\linewidth}{1pt} \begin{sffamily} \begin{itemize} \item \index{reference!how to add!by hand}You will now be presented with a window in which to type the name of your new library. \textbf{Open} your new library in a sensible place (the desktop?) and save it as ``TEST''. \item Choose \textbf{References $\mid$ New}. \end{itemize} Now you have a window in which to insert the various elements of a journal article reference. \index{template!reference templates}EndNote provides a variety of citation templates with slots for you to fill for sources such books and personal communications and theses---even, lately, computer programs. You can choose the appropriate template for the reference you are typing in from the drop-down box at the top of the window. For this example, you are going to use the default, ``\textbf{Journal Article}'' so you don't have to do anything. Just for the sake of practice, you are going to try typing in the details of the following paper: \begin{quotation} J. D. Watson and F. H. C. Crick, ``A structure for Deoxyribose Nucleic Acid'', Nature (1953), volume 171, p737 \end{quotation} The \textbf{New Reference} window opens with the cursor in the ``\textbf{Author}'' field of the blank entry so you can type the name of the first author straight away, namely: \begin{quotation} \textbf{Watson, J. D.} \end{quotation} Don't forget the punctuation. \begin{itemize} \item Hit the ``ENTER'' or ``RETURN'' key (often labelled \fbox{$\hookleftarrow$} to move to the next line down in the Author field and enter Francis Crick's name next, also surname-first. \item Then use the tab (\fbox{$\rightarrow\!\mid$}) key to move to the next field, ``\textbf{Year}''. \end{itemize} \ldots and so on. If, as for the ``\textbf{Issue}'' space in this example, a field should be blank, just tab into the next field that you \emph{can} fill and type that value in. I could go into detail about how to type values into the various fields, but you would do better to ``RTFM'' (``Read The Flipping Manual'') as we geeks say. Read the section in the EndNote manual about inputting references at least once---if you enter references incorrectly at the start of building your library you are going to make a lot of work for yourself in the future. The basic rules-of-thumb are: \begin{itemize} \item Enter names, one-per-line in the ``surname first'' format: \begin{quotation} \textbf{Watson, James D.} \end{quotation} This is a more reliable way to record authors than first-name-first, especially when dealing with ``van der Valk''s and the like. \item Don't waste time trying to enter special formatting or symbols (there is some provision for Greek letters in titles and certain symbols in names, however). \item Don't use ``\textit{et al}'' to avoid inputting long lists of authors. Put all their names in for later reference---unless, of course, there are hundreds. This way you let the program decide (according to the house style of the journal) when and how to abbreviate them. \item When you have finished, just \textbf{Close} the \te