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I'm in the humanities, and I'm currently using zotero to cite primary and secondary materials in my dissertation. I apply the Chicago Manual Style, and don't have any issues with secondary sources.

I do have problems with primary documents. I use archival materials, so the standard practice in my field goes something like this:

"name document", archive, x, y, z, page.

However, zotero puts the archive at the end:

"name", x, y, z, page, archive.

Is there a way to change the citation code in zotero to correct it(while keeping the CM style)?

Or do I change everything manually (and risk messing up the footnotes)?

Thanks!

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Yes, you can. Zotero stores citation style information in a file format that is called Citation Style Language (CSL). You can download and adapt style files in this format from several repositories, such as this one, or create your own style files form scratch.

In order to add a CSL file to Zotero, follow these instructions from the Zotero wiki:

CSL styles (with a “.csl” extension) can also be added through the Style Manager, found under the “Styles” tab of the “Cite” pane in the Zotero preferences panel. It shows you which styles are already installed, and also allows you to add (by clicking the + button) and delete (by pressing the - button) styles. Another installation option is to drag-and-drop a CSL style file onto an open Firefox browser window.

On changing available citation styles within Zotero, the manual says:

When you click the “Insert Citation” button for the first time in a document, Zotero opens the Document Preferences, where you can select the citation style you want to use in your document. You can change the citation style at any point later by clicking the “Set Document Preferences” button.

I'm not familiar enough with the CSL syntax to explain which changes you would have to make in order for primary documents to appear the way you want. However, you may be able to find an adapted version of the Chicago style that suits your needs on a repository; or you can use the online CSL editor to tweak an existing Chicago style CSL file without having to deal with the syntax.

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