Burrete

A molecular file workspace with macOS Finder Quick Look previews, Mol* 3D, external xyzrender SVG rendering, RDKit molecule grids, Ketcher sketching, a source-built iPhone preview app, and a hosted OpenAI Mol* viewer.

What Is Burrete?

Burrete is a macOS desktop app, Finder Quick Look extension, and source-built iPhone preview app for molecular structure files. It is built for the small daily loop of computational chemistry, structural biology, and cheminformatics work: open a structure, confirm what it is, switch renderer when needed, compare files in tabs, and recover quickly when Quick Look or renderer caches need maintenance.

Use it in two ways:

• Finder previews: select a molecular file in Finder and press Space.
• Desktop workspace: open Burrete directly to inspect files in tabs, browse project folders, search commands and structures, sketch molecules, review collections, and send files to external chemistry tools.
• iPhone preview app: build the BurreteMobile Xcode target from source, then open molecular documents from Files or another iOS document provider.
• Public molecular plugin: preview an authorized molecular attachment or a public PDB entry directly in the Burrete workspace through ChatGPT or Codex.

Burrete is intentionally a compact utility, not a full molecular modeling environment.

Download

You can install Burrete with the Homebrew tap:

brew tap SergeiNikolenko/burrete
brew install --cask burrete

Check the cask version when you need to confirm a specific release:

brew info --cask SergeiNikolenko/burrete/burrete

For the latest stable GitHub release, use the Burrete Bun CLI:

bunx burrete latest
bunx burrete install
bunx burrete doctor

The Bun installer places Burrete in ~/Applications by default. Use bunx burrete install --system only when you intentionally want the app in /Applications for all users. If Finder previews do not appear after install, run bunx burrete doctor to check the app bundle, Quick Look extension, qlmanage, and installed version.

You can also download Burrete from the GitHub Releases page:

Download the latest Burrete release

1. Open the latest release.
2. Download the Burrete-<version>.zip file.
3. Unzip it.
4. Move Burrete.app to your Applications folder.
5. Open Burrete once from Applications.

Quick Start

After installation:

1. Open Burrete.app once so macOS registers the app and Quick Look extension.
2. In Finder, select a supported molecular file and press Space.
3. Open Burrete directly for the full workspace:
   • Cmd+O opens molecular structure files.
   • Cmd+P or / opens the command palette.
   • Cmd+, opens settings.
   • The sidebar browses project folders, nested structures, and recent files.
4. If previews do not appear, run:

bunx burrete doctor

Supported Files

Burrete supports several preview paths. Some formats open directly in Mol*, some use the RDKit grid runtime, and some require the external xyzrender renderer.

Path	Formats	Notes
Mol* interactive 3D	PDB, ENT, PDBQT, PQR, CIF, MMCIF, MCIF, BCIF, SDF, SD, MOL, MOL2, XYZ, GRO	Default path for most structure files. XYZ can also use xyzrender.
RDKit molecule grids	SDF, SD, SMILES, SMI, CSV, TSV	Collection view with search, sorting, SMARTS filtering/highlighting, selection, append/merge, and export.
External xyzrender	XYZ, CUB, CUBE, ABI, COM, FDF, IN, INP, LOG, NW, OUT, PSI4, QCIN, VASP, MAE, MAE.GZ, MAEGZ, CMS	Requires a local xyzrender executable. Used by default for single-frame XYZ and required for external-renderer-only formats.
Molecular dynamics / topology	XTC, TRR, DCD, NCTRAJ, LAMMPSTRJ, TOP, PSF, PRMTOP	Registered as molecular files and routed to Mol* where supported by the runtime.
OpenMM coordinate artifacts	XML, INPCRD, RST7, CRD, RST, STATE	Render as structures when standalone coordinates are present, with the raw text available in the document surfaces. System XML without positions falls back to text.
OpenMM workflow artifacts	PAR, PRM, RTF, STR, KEY, CHK, CHECKPOINT	Open as text/workflow artifacts. Binary checkpoints show metadata because OpenMM checkpoint payloads are tied to the matching system, platform, version, and hardware context.
FEP network workspace	GraphML	Opens a ligand network preview workspace rather than a standard molecule preview.

Multi-frame XYZ files stay in Mol* when Burrete detects trajectory content so the native trajectory controls can show the available frames. When you rotate a molecule in Mol* and switch to xyzrender, Burrete can pass the current orientation through the renderer handoff. CUBE, CIF, MMCIF, MCIF, XYZ, and external-renderer input previews expose an optional VESTA handoff when VESTA is installed.

Desktop Workspace

Opening Burrete directly gives you a compact molecular workspace:

• tabbed previews that keep renderer state alive while you switch files
• a project sidebar for folders, nested structures, recent files, and search
• a command palette for opening files, switching renderers, maintenance actions, exports, project navigation, Ketcher, and FEP network previews
• right and bottom docks for comparing structures, text files, Ketcher, grids, and workflow panels
• "Open In" actions for Finder, the default app, or discovered chemistry editors
• text-file viewing for logs, scripts, configs, and related project files

iPhone Preview App

The repository includes a source-built iPhone app target at ios/BurreteMobile. It is not part of the Homebrew macOS release, but it shares the project preview runtime and supports iOS document handoff through Files and "Open In" sheets.

The mobile app focuses on phone-first inspection:

• Apple-style file browser and document opening for molecular project files
• Mol* structure previews in a full-screen mobile viewer
• RDKit-rendered SDF grid and table previews
• trajectory and pose controls surfaced near the bottom of the viewport when a loaded document needs them
• app icon and document-type registration for supported molecular formats

See ios/BurreteMobile/README.md for the target layout, build command, signing notes, and real-device install flow.

Molecule Collections and Ketcher

Burrete includes an RDKit-powered collection grid for SDF, SMILES, CSV, and TSV files. The grid supports search, sorting, SMARTS filtering/highlighting, selection, infinite loading, append/merge workflows, and export.

The desktop app also includes a Ketcher small-molecule editor. You can sketch a molecule, import/export common small-molecule formats, send a sketch to Mol*, xyzrender, or a collection grid, and edit grid rows through Ketcher.

Macromolecule editing is not enabled in the current Ketcher integration.

Workspace Workflows

Beyond single-file previews, the desktop workspace includes focused workflows for structure triage:

• xyzrender sheets for comparing SVG-rendered structures and exported artwork
• docking and pose-review surfaces backed by the shared Mol* viewer runtime
• FEP network GraphML previews with ligand cards and grid handoff
• FEP setup panels for assembling ligand-network inputs

These workflows live in the desktop app. Finder Quick Look remains optimized for quick file previews.

Public Plugin and MCP

The hosted Burrete plugin exposes a public HTTPS MCP endpoint and renders molecular results directly in the Burrete workspace:

• Plugin documentation: https://burrete-landing.vercel.app/docs/plugin
• MCP endpoint: https://burrete-plugin.vercel.app/mcp
• Source: apps/burrete-public-plugin

Its read-only preview_molecular_file tool accepts one authorized PDB, ENT, PDBQT, CIF, mmCIF, SDF, SD, XYZ, or extended XYZ attachment. The preview_pdb_structure tool retrieves one public RCSB entry by PDB ID. Both return bounded model-visible composition data and render the raw structure only inside the sandboxed Burrete workspace. Files are limited to 3 MiB, processed in memory, and not written to Burrete application storage.

The hosted plugin and the local plugin live in this repository; there is no separate plugin source repository. Public installation through OpenAI's Plugins Directory becomes available after directory review and publisher release.

Burrete includes a Codex plugin that turns the local application into an agent-operable molecular workspace. The plugin bundles focused workflow skills with a typed local MCP server, so Codex can:

• open molecular structures, SDF collections, trajectories, and result bundles;
• observe the active document, tabs, panels, viewer readiness, and scene state;
• run allowlisted Mol* actions such as focusing ligands, hiding waters, changing representations, and resetting the camera;
• render bounded markdown, table, chart, and molecular-report panels beside the workspace;
• preserve local-file provenance without exposing an arbitrary shell or unrestricted file-access tool.

Install the self-contained plugin from this repository with:

bun run install:plugin

The installer stages a dedicated local marketplace and uses the current codex plugin marketplace add and codex plugin add flows when a working Codex CLI is available. Restart Codex after installation, then mention @Burrete or select it from Plugins.

See the hosted and local agent platform contract, the local plugin architecture and installation guide, and the public plugin guide. Burrete remains the canonical source repository for every application and MCP surface.

Settings and Maintenance

Burrete settings cover:

• General workspace defaults and open documents
• Appearance, themes, and preview backgrounds
• Keyboard shortcuts and command-palette navigation
• Structure rendering, including Auto, Mol*, and external xyzrender
• Stable and beta update checks
• Files, recent structures, and project folders
• Burrete/Codex integration status
• Quick Look reset, preview cache cleanup, logs, diagnostics, and maintenance

Optional integrations include a local xyzrender executable, VESTA, and external chemistry editors discovered by macOS.

Unsupported file or format?

If Burrete cannot open or preview a molecular file, please open an unsupported-file issue. Before submitting:

1. Search existing issues for the extension or format name.

2. Include the exact file extension, where the failure occurs, your Burrete and macOS versions, and the installation method.

3. On macOS, include the output of:

   mdls -name kMDItemContentType -name kMDItemContentTypeTree "/path/to/file"

4. Attach the smallest non-confidential sample that reproduces the problem. If the file is proprietary, do not upload it publicly; describe the format and offer to share a sanitized sample privately.

Docs

• Documentation map
• Changelog
• Installing and building from source
• Configuration
• Security and permissions
• Privacy policy
• Terms of use
• Renderer support
• Quick Look debugging
• iPhone preview app
• Contributing

License

MIT