Goal

Zettlr is set up for use in a broad range of academic fields, and I've found it necessary to customize a bunch of the default settings, including the export settings and a large autocorrect and (smaller) snippet library.

My hope is that this helps other chemists and biochemists to get started with Zettlr settings. To use, follow the Zettlr instructions for migrating computers. Only replace these files on a fresh install, before you've modified them! Otherwise, you'll have to figure out how to merge files properly.

An important note: Adding lots of KaTeX equations just to show special characters (i.e. $\beta$ decay) can really slow Zettlr's linter, so I've found that adding them as Unicode characters is a better idea. However, this limits which LaTeX --> PDF engines you can use. The older pdfTeX does not support unicode characters, but XeTeX and LuaTeX do.

Contents

• autocorrect.json - an extended list of autocorrects to allow insertion of UniCode greek letters and symbols.
• custom.css - Lightens the dark background of the Zettlr dark mode to make chemical structures with transparent backgrounds easier to read.
• LaTeX-chem.yaml - A zettlr/pandoc export formula to generate LaTeX files from zettlr with reasonable defaults for a chemical manuscript or notebook.
• LuaTeX-Chem-PDF.yaml - A zettlr/pandoc export formula to generate PDFs from Zettlr files; will work with the UniCode characters inserted by the autocorrect.json file.
• pdfTeX-Chem-PDF.yaml - a faster PDF export formula, but will not format directly inserted unicode characters (as used by autocorrects.json) properly.
• snippets
  • ce.tpl.md - allows use of :ce: to create a LaTeX chemequation block to properly format chemical formulas and equations.
  • titleblock.tpl.md - inserts a titleblock which can be tabbed through.
• backup-config.sh - A bash script to back up zettlr config files (tested on linux). Run script with no commands for usage.

Usage

To use individual files:

• .yaml export files can always be dragged and dropped into ~/.config/Zettlr/defaults
• Contents of the snippets directory can be copied into ~/.config/Zettlr/snippets
• Please check the contents of your current autocorrect.json and custom.css before overwriting the whole file!! If you have any prior modifications to either file, you will want to manually merge the files.
• autocorrect.json should be pasted into the autocorrect{...} block in your config.json file.
• Note that custom.css makes specific modifications to the light and dark themes, to make a "light sepia" theme, and a dark theme for which black chemical structures in transparent images (svgs and pngs) are still visible. These may be incompatible with other custom css you have applied.

Using update-config.sh will allow making a backup of your user-modifiable Zettlr config files to a separate directory, which can then be synced to another computer, or changes can be tracked with a git repo. Do not post the whole directory to a public repo, as it contains user-specific info.

Use on Windows

If using zettlr on Windows, if WSL is installed you can now specify the -w flag (it must be before the other flags in the sequence for...bash reasons) if on windows to back up from or restore to the Windows zettlr config directory (C:\Users\<username>\AppData\Roaming\Zettlr\).

Contributions

If you'd like to contribute other YAML files (either journal-specific manuscript export files, or other useful formats) feel free to create a PR.

Modifying the paths to work on WSL or Mac should be easy enough, if you do so and would like to contribute your versions to this repo, that'd be great.