# Talk:LaTeX template for PhD thesis

## FAQ: glossary troubleshooting

The glossary is difficult to get started. If you are in a hurry, consider writing it by hand. Here's what I did to get it going using the nomencl package. Jakob

#### changed in main doc

\usepackage{nomecl}

\makenomenclature % place this before /begin

\print nomenclature


#### how to place a nomenclature entry

\nomenclature[zcif]{$CIF$}{Cauchy's Integral Formula} % z for abbreviations (defined in .cls)

\nomenclature[sorting]{XYZ}{description}


#### how to generate the files required

Execute these commands directly via the LaTeX command line, e.g. the console in TeXShop.

makeindex  filename.nlo -s path/nomencl.ist -o filename.nls<br>
nomencl.ist = index style file

e.g. with full paths on my systems:<br>
/usr/local/gwTeX/bin/powerpc-apple-darwin7.9.0/makeindex thesis.nlo -s /usr/local/gwTeX/texmf.texlive/makeindex/nomencl/nomencl.ist -o thesis.nls

or define TexShop engine: ~/Library/TexShop/Engines/Nomencl.engine<br>
makeindex  "${1%%.tex}.nlo" -s /usr/local/gwTeX/texmf.texlive/makeindex/nomencl/nomencl.ist -o "${1%%.tex}.nls"<br>
chmod u+x Nomencl.engine


## FAQ: glossary, quick work-around

If you don't want to bother with the above to get nomencl package to work, just do the glossary by hand. You will lose the ability to define glossary words at any position in the text but may save yourself some time.

\begin{multicols}{2} % \begin{multicols}{#columns}[header text][space]  produces a 2 column page for a compact glossary
\begin{footnotesize} % scriptsize(7) < footnotesize(8) < small (9) < normal (10)

BAC - bacterial artificial chromosome; circular DNA vector used to propagate large inserts in bacteria\\  % double backslash produces a free line; without it glossary entries will be directly connected but indented like paragraphs.

cDNA - complementary DNA; reverse transcribed from mRNA, essentially a DNA copy of an mRNA, usually spliced, i.e. containing exon sequences only\\

DAPI - 4’,6-diamidino-2-phenylindole; a ﬂuorescent stain that binds strongly to DNA and serves to marks the nucleus
in ﬂuorescence microscopy\\

\label{nom} % target name for links to glossary

\end{footnotesize}
\end{multicols}


## FAQ: empty page after section

The template appends an empty page to a section if it ends on an odd page number. This is not bug but a feature to allow all section start pages to start on an odd page, i.e. a page that faces you when you open the thesis or flip a page.

More precisely, the template does this because it uses "book" style document. If you want to avoid this, use the "report" style document. You can find the instructions how to change this in the file PhDtemplateLATEX\Latex\Classes\PhDthesisPSnPDF.cls of the template.

## FAQ: compiler error in nomencl package

Francesco reported a problem when compiling the template. He said:

"!Latex error: unknown option 'intoc' for package 'nomencl'
1.97  \ProcessOptions\relax"


I guess the simplest way short of trying to correct the problem would be to do without the glossary. Nomencl generates the glossary which is quite hard to get to run anyway. I think you can probably save valuable time by just writing the glossary by hand and commenting out the nomencl code from the template. If you decide to correct the problem, you would have to check whether you have the nomencl package properly installed - not all LaTeX installations have all packages used in this template. If that still doesn't solve the problem I would post your problem on latex/tex discussion forums where the real experts (not me) hand out.

Hope that helps, Jakob 07:18, 24 August 2009 (EDT)

## FAQ: how to change the brackets of cited references in the text

If you want to change the brackets so that when you use \cite{reference}, [1] is shown instead of (1), go to this file PhDtemplateLATEX\Latex\Classes\PhDthesisPSnPDF.cls, find the following line:

\usepackage[round, sort, numbers]{natbib}


and erase "round" (square brackets are by default).