The majority of the documentation for EMAN2 is made using LATEX (see the http://www.latex-project.org/LATEX homepage for more information). No preamble should be included in the new documentation; preamble information can removed either manually or using the python script rm_preamble.py (see 3.8.2 for more information).
Documentation can be created using a WYSIWYG LATEX editor such as http://www.lyx.org/LyX or http://www.www.texmacs.org/TeXmacs. When using these utilities do not create title pages, abstract sections, or tables of content as this will cause integration problems with the rest of documentation.
The recommended steps for adding new documentation go as follows: