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Exporting a Manuscript

While you write, the document stores only your text and CiteDesk's markers, not the typeset citations and bibliography. When the manuscript has to go out, Export Manuscript produces a separate file in which the citations, footnotes and bibliography are real, finished content. Exporting never changes the original Markdown document.

Formats

Choose File > Export Manuscript… (or Export on the document card in the right pane), then choose the format, whether to append a bibliography and its heading, and, for Word and PDF, the paper size, and then the place to save. There are four formats: Word, PDF, HTML and Markdown. The style, language, romanization and footnotes or endnotes all come from the document's document preferences; the export window has no separate settings for them.

When the export finishes, a notification at the top of the window tells you how it went, including the points that need your attention described below. If there is nothing to note, it disappears after a few seconds; otherwise it stays until you click Got it.

Word

The footnotes or endnotes in the Word file are real footnotes or endnotes, and the bibliography consists of real paragraphs, formatted (italics, small caps and so on) as the style prescribes. Every citation cluster and the bibliography carry Zotero field codes, so with the Zotero plugin installed in Word you can keep refreshing and editing the citations with Zotero; without the plugin the file is an ordinary Word document.

Notes:

  • A narrative citation has no corresponding data structure in Zotero and is written as an ordinary citation; after a refresh in Zotero it becomes parenthetical.
  • Uncited references added to the bibliography with Edit Bibliography are dropped when Zotero reads the file.
  • Changing a citation in Word does not flow back to the Markdown source; the source is the authority.
  • Formulas are written as editable Word equations where possible; those the converter cannot handle stay as images, and the completion notice says how many of each.

PDF

The PDF is printed from the same HTML. With a footnote style, each footnote is printed at the foot of the page it belongs to; with an endnote style, or when the document has no notes, the notes are printed together at the end. The paper size is chosen in the export window, and headers, footers and page numbers are laid out by the application.

HTML

The HTML is one self-contained file with images and formulas embedded; notes are placed at the end and can be followed back and forth by clicking.

Markdown

The Markdown manuscript replaces citations with the text produced by the style, writes footnotes as standard footnotes such as [^citedesk-1], and appends the bibliography and the footnote definitions at the end. Citations, notes and bibliography entries are written as plain text, with the same characters the style produced; characters that would be misread as Markdown are escaped so that the rendered text stays unchanged.

If a citation or annotation is written inside the text of a Markdown link or image, the footnote number in the manuscript collides with the link: the number cannot be a link as well, so the text after it falls out of the link or the number shows up as a literal [^citedesk-N]. The application does not move these footnote numbers for you. The diagnostics in the right pane list each occurrence, and clicking one takes you to the place in the text; the notification at the end of an export also reports how many there are. Move those markers out of the link text before exporting.

Creating citations and bibliographies

Create Bibliography from References… (in the context menu once references are selected in the library) corresponds to Zotero's Create Citations/Bibliography: choose a style and a language and copy the citations or the bibliography of the selected references to the clipboard (as rich text and plain text together), save them as RTF or HTML, or print them. Quick Copy on the Export page of the settings, and Copy Citation and Copy Bibliography in the Edit menu, produce the same output.