The package mmap does a little bit more than cmap, it also works for mathematical symbols in your pdf.
So if your pdf does not use mathematics use \usepackage{cmap}. If you have problems with ligatures further on with computer modern use \usepackage[resetfonts]{cmap}. With mathemtic symbols use \usepackage{mmap}. If you have still problems use \usepackage[noTeX]{mmap}.
The differences are:
\usepackage{cmap}: accepted preloaded fonts without reloading.\usepackage[resetfonts]{cmap}: as you can read in the README of cmap this forces the reloading of preloaded fonts (Computer Modern).\usepackage[useTeX]{mmap} and \usepackage{mmap}: does everything cmap does plus correcting mathematical symbols in your pdf; uses new -m.cmap files ("uses ascii strings for the macro-names").\usepackage[noTeX]{mmap}: does everything cmap does plus correcting mathematical symbols in your pdf; uses the cmap files (unicode).Load cmap or mmap first, then fontenc and babel.
The documentation of fixltx2e does only say "load in the preamble". I had no problems loading it after fontenc, babel and the used fonts.
To do your own experiments use the follwing MWE:
\listfiles % shows used files
\documentclass[12pt]{scrartcl}
%\usepackage{cmap} % pure T1 fonts
%\usepackage[resetfonts]{cmap} % pure T1 fonts, reset CM
%\usepackage{mmap} % cmap + mathematics (ASCII)
%\usepackage[noTeX]{mmap} % cmap + mathematics (Unicode)
\usepackage[Latin9]{inputenc} % or utf-8
\usepackage[T1]{fontenc} % font encription
%\usepackage[T3,T1]{fontenc} % T3 for package tipa
%\usepackage{tipa} % Phonetic alphabet
\usepackage[ngerman]{babel} % neue deutsche Rechtschreibung
%\usepackage{lmodern} % Latin Modern
%\usepackage{tgpagella} % has no virtual fonts
%\usepackage[osf]{mathpazo} % Minuskelziffern okay
%\usepackage{libertine} % Libertine Legacy (with virtual fonts)
\usepackage[osf]{libertine} % mit Medivalziffern bzw. Minuskelziffern
\newcommand*{\III}{\libertineGlyph{Threeroman}}
\newcommand*{\IV}{\libertineGlyph{Fourroman}}
\begin{document}
Römische Zahlen: \III, \IV.
\textsc{Ligaturen}: auffliegen auffinden finden Auflage Schifffahrt.
\textsc{Korrekt}: auf\/fliegen auf\/finden finden Auf\/lage Schiff\/fahrt.
Ziffern: 0123456789.
Donau Donaudampfschiff Donaudampfschifffahrt Donaudampfschifffahrtskapitän
Donaudampfschifffahrtskapitän
Donaudampfschifffahrtskapitän Donaudampfschifffahrtskapitän
Donaudampfschifffahrtskapitän Donaudampfschifffahrtskapitän
%\textipa{[\!b] [\:r] [\;B]}
\end{document}
Set or delete the comment sign to test cmap and mmap with or without fontenc and different fonts.
BTW: "Donaudampfschifffahrtskapitän" is a German word, good to get hyphenations.
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