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Overview

Burette Documentation

Burette is a macOS desktop app, Finder Quick Look extension, source-built iPhone preview app, local Codex plugin, and hosted public plugin 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.

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

What you can do

  • Press Space in Finder to preview supported molecular files.
  • Open the desktop workspace to inspect files in tabs, browse folders, search commands and structures, sketch molecules, edit text and structure sources in place, and route files or molecule records with target-aware drag and drop.
  • Use Mol* for interactive 3D structures, trajectories with smoothed playback, structure superposition, Maestro/PyMOL-style structure operations, and multi-state MolViewSpec Stories.
  • Open cell-scale crowded scenes (molj, molx, .mesozip) in the dedicated Mesoscale viewer.
  • Search, select, edit, append, merge, analyze, and export SDF, SMILES, CSV, TSV, DataWarrior, RXN, and RDF collections in grid and reaction-aware workspaces.
  • Run native Apple Silicon compute without external installs: clustering, similarity search, conformers, MMFF optimization, semiempirical energies, and the Chemical Space map with Metal-accelerated embeddings.
  • Review linked 2D/3D Chemical Space selections and activity cliffs beside the source collection.
  • Read PDF, DOCX, XLSX, PPTX, CSV, image, markdown, code, text, and email artifacts through the Retab-based file viewers.
  • Keep project folders current with the filesystem watcher and inspect Codex/Claude integration status in the Agents panel.
  • Inspect mass spectra (MGF, MSP, mzML, and more) in a dedicated spectrum viewer.
  • Use external xyzrender for formats that need artwork-style SVG rendering.
  • Run local xTB calculations (with an app-managed Conda install) for a small structure or selected molecular object.
  • Generate conformer ensembles with local CREST and optionally prune existing XYZ/SDF ensembles with PRISM.
  • Build the iPhone preview app from source when you need iOS document handoff.
  • Connect Codex to the local molecular workspace through focused skills and typed MCP tools, or preview attachments and public PDB entries through the hosted ChatGPT plugin.

Platform scope

SurfaceBest forImportant boundary
macOS desktopTabs, projects, drag and drop, grids, Ketcher, docking/FEP workspaces, native compute and Chemical Space, xTB, CREST/PRISM, exports, and diagnosticsFull workflow surface; external engines must be installed locally (managed install available for xTB).
Finder Quick LookA fast preview from Finder with SpacePreview surface, not the full desktop workflow.
iPhone source targetOpening supported documents from Files and inspecting mobile previewsBuilt from source; not included in the macOS Homebrew release.
Codex plugin and MCPTyped local workspace observation, opening, viewer control, and bounded report panelsPurpose-built tools, not arbitrary shell or unrestricted file access.
Hosted ChatGPT pluginPreviewing one authorized molecular attachment or public PDB entry, applying bounded scene actions, and editing an ephemeral Ketcher structureStructure tools are read-only; Ketcher state is bounded, revision-checked, ephemeral, and not a persistent web workspace.
  1. Install Burette
  2. Open your first file
  3. Choose the right surface
  4. Learn target-aware drag and drop
  5. Work with SDF and molecule collections
  6. Use native compute and Chemical Space
  7. Run xTB calculations
  8. Generate conformers with CREST
  9. Check supported formats
  10. Install the Codex plugin and MCP integration
  11. Fix Quick Look registration
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