Zettlr Setup Guide

Zettlr is the drafting tool in this workflow, built for linear academic manuscripts with citations and export paths.

Benefits for Research Memex users:

• @citekey autocomplete using your Better BibTeX citation keys from Zotero
• LaTeX math formulas rendered in real time
• Visual table editor for results and comparisons
• Export to Word, PDF, and LaTeX for journal submission
• Projects for organizing multi-chapter documents
• Open source with no vendor lock-in

Both tools open the same plain markdown files, so you can move between them at any point. This is about where a task is comfortable, not about what either one can do.

Typical workflow:

Zotero          Research Rabbit      Obsidian           Zettlr           Journal
(References) →  (Discovery)      →   (Synthesis)    →   (Drafting)   →   (Submission)
                                     [Web of notes]     [Linear paper]

1.1 download and install

1. Visit zettlr.com/download
2. Download for your operating system (macOS, Windows, Linux)
3. Install the application
4. Launch Zettlr

1.2 first launch configuration

1. Choose a workspace folder (can be the same as your Obsidian vault or separate)
2. Select your preferred theme (Light or Dark)
3. Configure editor settings (line numbers, spellcheck language)

This step connects Zettlr to your Zotero library through Better BibTeX.

2.1 export Better BibTeX library from Zotero

1. In Zotero: File → Export Library
2. Format: Better CSL JSON (recommended) or Better BibTeX
3. Check: "Keep updated" (auto-sync when library changes)
4. Save location: Choose a stable location like:

   /Users/[username]/Zotero/exports/My-Library.json

   Copy
5. Click OK

2.2 configure citation database in Zettlr

1. In Zettlr: Preferences → Export
2. Under "Citation Database":
   • Click "Add Database"
   • Navigate to your exported library file (e.g., My-Library.json)
   • Click "Open"
3. Verify: You should see the database path listed

2.3 test citation autocomplete

1. Create a new file in Zettlr
2. Type @ followed by a few letters from any author's last name
3. You should see autocomplete suggestions!
4. Select a citation → it inserts as [@smith2024a]

2.4 configure citation style

1. Preferences → Export → Citation Style
2. Default is Chicago style
3. To change: Download .csl file from Citation Style Language
4. Common academic styles:
   • APA 7th edition
   • MLA 9th edition
   • Harvard
   • IEEE
   • Nature
   • Your journal's specific style

3.1 citations with @citekey

Basic citation syntax:

• Parenthetical: [@smith2024a] → (Smith, 2024)
• In-text: @smith2024a → Smith (2024)
• With page: [@smith2024a, p. 45] → (Smith, 2024, p. 45)
• Multiple: [@smith2024a; @jones2024b] → (Smith, 2024; Jones, 2024)

Autocomplete features:

• Type @ and start typing author name
• Use fuzzy search (type @smi to find Smith, Smithers, etc.)
• Press arrow keys to select and Enter to insert
• Bibliography auto-generates in preview

Example workflow:

As @coviello2024 argues, organizational scaling requires...

However, this view has been contested [@mithani2023; @sanasi2025],
particularly regarding digital business models.

The framework proposed in [@palmie2023, pp. 234-236] suggests...

3.2 math formulas with LaTeX

Inline math:

The regression model is $y = \beta_0 + \beta_1 x + \epsilon$

Display math:

$$
\begin{aligned}
E[Y|X] &= \beta_0 + \beta_1 X \\
R^2 &= 1 - \frac{SS_{res}}{SS_{tot}}
\end{aligned}
$$

Common use cases:

• Statistical models
• Economic equations
• Mathematical proofs
• Chemical formulas
• Algorithmic notation

Zettlr renders LaTeX math in real time, which makes equations easier to check while drafting in Markdown.

3.3 visual table editor

1. Click the "Insert Table" button (or Cmd/Ctrl+T)
2. Select grid size (rows × columns)
3. Edit cells directly - Tab to navigate
4. Right-click for options:
   • Add/remove rows
   • Add/remove columns
   • Align columns (left/center/right)

Example use case:

| Model | AIC | BIC | R² |
|-------|-----|-----|-----|
| Model 1 | 245.3 | 267.8 | 0.42 |
| Model 2 | 238.1 | 264.9 | 0.51 |

3.4 comments for drafting

Add Hidden Notes:

This section discusses the methodology. <!-- Example: TODO reminder for later revision -->

Our findings suggest that... <!-- Example: Check citation against source -->

Keyboard shortcut: Cmd/Ctrl+Shift+C

Use cases:

• Leave notes to yourself
• Mark sections for revision
• Hide text temporarily without deleting
• Add reviewer responses (invisible in export)

Projects help you organize dissertations, book chapters, or multi-section papers.

4.1 create a project

1. Create a folder structure:

   /My-Dissertation/
   ├── 01-Introduction.md
   ├── 02-Literature-Review.md
   ├── 03-Methodology.md
   ├── 04-Results.md
   ├── 05-Discussion.md
   └── 06-Conclusion.md

   Copy

2. Right-click the folder → Properties

3. Check "Treat as project"

4. Folder turns red with special icon

4.2 configure project export

1. Click the folder
2. Configure:
   • Title page information
   • Export formats (PDF, DOCX, etc.)
   • Table of contents settings
   • Bibliography options

4.3 compile your paper

1. Right-click project folder → Export Project
2. Zettlr concatenates all files in order
3. Generates single output with:
   • Proper citations
   • Formatted bibliography
   • Table of contents
   • Page numbers

Work on dissertation chapters separately, using Obsidian for research and Zettlr for drafting, then compile them into one document.

5.1 export to PDF (via LaTeX)

Prerequisites:

• LaTeX distribution installed (MacTeX, MiKTeX, or TeX Live)

Steps:

1. Cmd/Ctrl+E or click "Share" icon
2. Choose "PDF (LaTeX)"
3. First export may take time (downloading packages)
4. Result: Professional PDF with formatted bibliography

5.2 export to Word (.docx)

No LaTeX required:

1. Cmd/Ctrl+E → "Word (docx)"
2. Opens in Microsoft Word or compatible app
3. Citations formatted according to CSL style
4. Bibliography auto-generated at end

Use cases:

• Journal submissions requiring Word
• Collaboration with non-markdown users
• Track changes and comments in Word

5.3 export to LaTeX source

For advanced users:

1. Export → "LaTeX"
2. Generates .tex file
3. Compile with your own LaTeX editor
4. Full control over LaTeX formatting

5.4 configure export settings

Preferences → Export:

• Paper size: A4 or Letter
• Font: Choose academic font (Times, Palatino)
• Line spacing: 1.5 or 2.0 for drafts
• Bibliography style: Select your .csl file
• Remove ZKN IDs: Check this for clean output

6.1 from Obsidian to Zettlr

Scenario: You've synthesized findings in Obsidian. Now write the paper.

Workflow:

1. In Obsidian: Create synthesis notes with main arguments
2. Copy to Zettlr: Create new .md file for paper section
3. Transform: Convert bullet points → paragraphs
4. Add citations: Use @citekey for every claim
5. Export: Generate PDF/Word when ready

Example:

<!-- In Obsidian (synthesis note) -->
## Key Theme: Scaling requires both strategy and structure
- Coviello 2024: Distinguishes scalability from scaling
- Mithani 2023: Digital vs non-digital models differ
- Sanasi 2025: Experimentation structures growth

<!-- In Zettlr (paper draft) -->
The literature reveals that successful scaling requires both
strategic vision and organizational structure [@coviello2024].
This is particularly evident in the distinction between digital
and non-digital business models [@mithani2023], where the role
of experimentation differs significantly [@sanasi2025].

6.2 from AI conversations to structured sections

1. Export Cherry Studio conversations to markdown
2. Review AI-generated synthesis
3. Copy useful passages to Zettlr
4. Add proper citations. AI can hallucinate these.
5. Verify every claim against your Zotero library

6.3 Zotero → Zettlr direct citations

No copy-paste needed:

1. Know your citation key from Zotero (e.g., smith2024a)
2. In Zettlr: Type @smith → autocomplete suggests it
3. Select → inserts [@smith2024a]
4. Export → bibliography auto-generated

7.1 when to switch from Obsidian to Zettlr

The trigger is a clear paper outline: once the argument has a shape and you are ready to draft linear sections, move the draft over. The task-by-task split is at When to use Zettlr vs Obsidian.

7.2 file organization strategy

Recommended Structure:

/Research-Papers/
├── Drafts/
│   ├── Paper-2025-Scaling/
│   │   ├── 01-Introduction.md
│   │   ├── 02-Literature.md
│   │   ├── 03-Methods.md
│   │   └── ...
│   └── Dissertation/
│       ├── Chapter-1-Introduction/
│       └── Chapter-2-Theory/
├── Submitted/
└── Published/

7.3 version control with git

Zettlr files are plain markdown, which makes them suitable for Git.

Workflow:

cd /Research-Papers/Paper-2025-Scaling/
git init
git add *.md
git commit -m "Initial draft of introduction"

Benefits:

• Track every revision
• Revert to earlier versions
• Collaborate via GitHub
• Never lose work

7.4 collaborative writing

Option 1: Git-Based (Technical)

• Push to GitHub private repo
• Collaborators pull, edit, push
• Merge changes
• Requires Git knowledge

Option 2: Export to Word (Simple)

• Export to .docx
• Share via email/cloud
• Collaborators use Track Changes
• Import revisions back to markdown

Essential shortcuts:

• Cmd/Ctrl+E: Export document
• Cmd/Ctrl+B: Bold
• Cmd/Ctrl+I: Italic
• Cmd/Ctrl+K: Insert link
• Cmd/Ctrl+Shift+C: Insert comment
• Cmd/Ctrl+T: Insert table
• Cmd/Ctrl+F: Search
• Cmd/Ctrl+R: Replace

Citation Shortcuts:

• Type @ → Citation autocomplete
• Type # → Headings
• Type $ → Inline math
• Type $$ → Display math

9.1 zettelkasten IDs (optional)

Zettlr supports Zettelkasten-style linking:

• Format: [[202501151420]] (timestamp-based IDs)
• Auto-generated with Cmd/Ctrl+L to create a unique identifier for each note

9.2 custom CSS for styling

1. Preferences → Display → Custom CSS
2. Add custom styles for preview
3. Example: Change heading colors, font sizes, etc.

9.3 snippet manager

Create reusable text snippets:

1. Preferences → Snippets
2. Add snippets with shortcuts
3. Examples:
   • @@email → your email address
   • @@affiliation → your institution
   • @@template → paper template structure

Citation library not loading

Symptoms: @citekey autocomplete doesn't work

Solutions:

• Verify library path in Preferences → Export
• Check file format (must be CSL JSON or BibTeX)
• Re-export from Zotero with "Keep updated"
• Restart Zettlr

Export to PDF fails

Symptoms: "LaTeX not found" error

Solutions:

• Install LaTeX distribution:
  • macOS: MacTeX (4GB) or BasicTeX (100MB)
  • Windows: MiKTeX
  • Linux: TeX Live
• Or export to Word instead (no LaTeX needed)

Bibliography not appearing

Symptoms: Citations work but no bibliography at end

Solutions:

• Ensure citation style (.csl) is selected
• Check that you have at least one citation in the document
• Try exporting to different format
• Verify Better BibTeX export is up-to-date

Math formulas not rendering

Symptoms: LaTeX math shows as plain text

Solutions:

• Check syntax: no spaces after $ in inline math
• Verify you're in preview mode (Cmd/Ctrl+Alt+E)
• Test with simple formula: $x^2$
• Check KaTeX documentation for supported commands

Complete workflow example

Phase 1: Research (Weeks 1-4)

• Zotero: Collect 50+ papers, configure Better BibTeX
• Research Rabbit: Expand citation network
• Obsidian: Take literature notes, synthesize themes

Phase 2: Analysis (Weeks 5-8)

• Cherry Studio: Pattern analysis with AI support
• Obsidian: Build conceptual framework
• Zotero: Refine collection, verify citations

Phase 3: Writing (Weeks 9-12)

• Zettlr: Draft paper sections
  • Use @citekey for every claim
  • Add math formulas where needed
  • Build results tables
• Export: Generate PDF for advisor review

Phase 4: Revision (Weeks 13-16)

• Zettlr: Incorporate feedback
  • Use comments for tracking changes
  • Update citations
  • Refine arguments
• Export: Final submission to journal

Tool handoff points

From Obsidian to Zettlr:

1. Identify completed synthesis notes in Obsidian
2. Create new Zettlr file for paper section
3. Copy main arguments and evidence
4. Transform from notes → prose
5. Add proper citations with @citekey

From Zettlr back to Obsidian:

1. Export Zettlr paper to markdown
2. Save in Obsidian vault for archiving
3. Link to related research notes
4. Track published work

By the end of this guide, you should have:

• Installed Zettlr
• Connected to Zotero Better BibTeX library
• Tested @citekey autocomplete
• Configured citation style (e.g., APA, MLA)
• Created a test document with citations
• Inserted a math formula (if needed)
• Created a table
• Exported to PDF or Word successfully
• (Optional) Created a project for multi-file paper
• (Optional) Installed LaTeX for PDF export

# Test Paper

As @[yourcitekey] demonstrates, the methodology...

The model is: $y = \beta x + \epsilon$

## References
(Auto-generated)

Task split: When to use Zettlr vs Obsidian.

Essential keyboard shortcuts

Zettlr documentation

• Citation Guide
• Tables
• Math Formulas
• Projects
• Exporting
• Writing Markdown in Zettlr
• File Renaming (Zotero)

Integration with other tools

• Zotero Setup Guide - Configure Better BibTeX citation keys
• Obsidian Setup Guide - Research note-taking
• Cherry Studio Setup Guide - Pattern analysis with AI support

External resources

• Citation Style Language - Download .csl files for any journal
• Pandoc Documentation - Zettlr's export engine
• KaTeX Documentation - Math formula reference
• Zettlr Forum - Community support

Q: Should I use Zettlr OR Obsidian? A: Both - they complement each other. The task split is at When to use Zettlr vs Obsidian.

Q: Can I use the same folder for both? A: Yes, but not recommended. Keep research notes (Obsidian) separate from paper drafts (Zettlr) for clarity.

Q: Do citation keys work the same way? A: Yes. Both use Better BibTeX citation keys from Zotero. Configure once in the Zotero guide, then use the same keys everywhere.

Q: Is Zettlr required for Research Memex? A: No, it's optional. But if you're writing papers (not just taking notes), Zettlr makes citations and export much easier than Obsidian.

Q: Can I write my entire dissertation in Zettlr? A: Yes. Use Projects to organize chapters, then compile into a single PDF or Word document.

1. Install Zettlr and connect to your Zotero library
2. Create a test document with 3-5 citations
3. Export to PDF or Word to verify setup
4. Start drafting your next paper section in Zettlr
5. Keep using Obsidian for research notes and synthesis

Research in Obsidian, draft in Zettlr, and export to journals; Better BibTeX keeps the citation keys consistent across both tools.