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I am trying to get the PDF output of my thesis with bookmarks using hyperref package. I am able to get the sections and subsections displayed in bookmark however the chapter is not displayed. How can I get the chapter title displayed in this PDF output?

\documentclass[12pt]{report}
\setcounter{secnumdepth}{5}
\setcounter{tocdepth}{5}


\usepackage{uncc-thesis}
\usepackage{subfig}
\usepackage{amsmath}
\usepackage{mathtools}
\usepackage{graphicx,epstopdf}
\usepackage{rotating} 
\usepackage{float}
\usepackage{color}
\usepackage[numbers, square, comma, sort&compress]{natbib}
\bibpunct{[}{]}{,\!}{n}{}{;}
\usepackage[breaklinks=true, bookmarks=true, pdftoolbar=true, linktocpage=true,colorlinks=true,citecolor=blue]{hyperref}

\usepackage{setspace}
\usepackage{tocloft}
\usepackage[font=small,format=plain,labelfont=bf,textfont=it]{caption}

\begin{document}

\pdfbookmark[0]{Abstract}{abstract}
\begin{abstract}
This is the abstract.
\end{abstract}

\pdfbookmark[0]{Dedication}{dedication}
\dedication
Here is the dedication.

\pagebreak{}
\pdfbookmark[0]{Acknowledgements}{acknowledgements}
\acknowledgments
Here is the acknowledgement.

\begin{singlespace}

\clearpage
\phantomsection
\tableofcontents
\label{toc}
\clearpage

\phantomsection
\listoftables
\label{lot}
\clearpage

\phantomsection
\listoffigures
\label{lof}
\end{singlespace}


\pagebreak{}
\pdfbookmark[0]{List of Abbreviations}{listofabbreviations}
\listofabbreviations
\input{List-of-Abbreviations}

\pagebreak{}
\pdfbookmark[0]{List of Symbols}{listofsymbols}
\listofsymbols
\input{List-of-Symbols}

\include{Chapter_One}

\include{Chapter_Two}
\include{Chapter_Three}
%\include{Chapter-Four}
%\include{Chapter-Five}


\bibliographystyle{ieeetr}

\bibliography{PhDThesis_Bibtex_Final} % References file

\end{document}
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2  
This example is far from minimal. And the most important part, the code for the chapters, is even missing :-) I removed every package I don't have and everything which gave errors and created a file Chapter_One containing a chapter and some sections et voila, I get the chapter title in the bookmarks list. I suggest you remove stuff from your preamble until the bookmarks appear. This way you'll immediately find the reason. –  Stephan Lehmke Apr 11 '12 at 20:50
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1 Answer

As others have said, you should load hyperref last of all your packages (you should also load subfig after caption). However, that alone doesn't fix the problem here. The redefinition of \@chapter in uncc-thesis.sty causes the bookmarks to disappear.

This seems to fix the problem. The uncc-thesis package is loaded, then \@chapter is redefined (again) and finally hyperref is loaded. The trick with MakeUppercase{\gdef... is explained here.

\usepackage{uncc-thesis}

\makeatletter
\def\@chapter[#1]#2{\ifnum \c@secnumdepth >\m@ne
                         \refstepcounter{chapter}%
                         \typeout{\@chapapp\space\thechapter.}%
                         \MakeUppercase{\gdef\noexpand\@temp{#1}} %NEW - puts an upper case 
                                                                  %version of #1 in \@temp
                         \addcontentsline{toc}{chapter}%
                                   {\protect{\@chapapp~\thechapter:\ \@temp}}% CHANGED
                    \else
                      \addcontentsline{toc}{chapter}{#1}%
                    \fi
                    \chaptermark{#1}%
%                    \addtocontents{lof}{\protect\addvspace{10\p@}}%
%                    \addtocontents{lot}{\protect\addvspace{10\p@}}%
                    \if@twocolumn
                      \@topnewpage[\@makechapterhead{#2}]%
                    \else
                      \@makechapterhead{#2}%
                      \@afterheading
                    \fi}
\makeatother

\usepackage[breaklinks=true, bookmarks=true, pdftoolbar=true, linktocpage=true,colorlinks=true,citecolor=blue]{hyperref}
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