JLmol

A powerful desktop application for molecular visualization built with Electron and JSmol. Experience native performance with advanced 3D visualization capabilities across all platforms.

Available for Windows • macOS • Linux

Powerful Features for Molecular Science

Everything you need to visualize, edit, and analyze molecular structures.

🧬

Advanced 3D Visualization

High-quality, interactive 3D rendering of molecules with multiple display styles (ball & stick, spacefill, etc.).

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🔍

PubChem Database Integration

Directly search and load molecules from the PubChem database by name, formula, or ID.

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✏️

Structure Editing Suite

Create and modify molecules with a 2D editor, a 3D ModelKit, and a live-preview XYZ editor.

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⚛️

Orbital Visualization

Analyze quantum chemistry results by visualizing molecular orbitals, including HOMO/LUMO levels.

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📁

Multi-Format Support

Load and save structures in various common formats like XYZ, PDB, MOL, CIF, and MOLDEN.

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ElemCo.jl Integration

Generate inputs and run quantum chemistry calculations with ElemCo.jl directly from the app, with local and remote execution support.

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⚗️

Semiempirical Calculations

Compute energies and optimize geometries with xtb's g-xTB method in one click, including constrained optimization that freezes selected atoms.

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🎯

Interactive Atom Selection

Click atoms in the 3D structure or the XYZ viewer to select them, with two-way sync, and insert them as an index list into your ElemCo.jl input.

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What's New

Highlights from recent releases. See the full changelog for every change.

July 2026 · v1.5.0

ElemCo.jl Input Builder

Assemble a calculation from ordered building blocks, browse and set every ElemCo.jl option (defaults and descriptions included), compose methods with spin prefixes (UCCSD, ΛCCSD(T), EOM-UCCSD), and work from a geometry or an FCIDUMP file — with Julia syntax highlighting.

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May 2026 · v1.4.0

Semiempirical Calculations with xtb / g-xTB

Calculate the energy or optimize the geometry of the current structure with the g-xTB method in one click. Set charge, unpaired electrons, and extra flags, and even freeze atoms to relax only a selected region.

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May 2026 · v1.4.0

Click-to-Select Atoms

Click atoms in the 3D structure or the XYZ viewer to select them, with the selection mirrored in both views. Insert the selected atoms as a 1-based index list into your ElemCo.jl input, or use them to constrain an xtb optimization.

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View all updates →

See JLmol in Action

Experience the power of JLmol with our interactive online demo. Load molecular structures, explore 3D visualizations, and test the editing capabilities directly in your browser.

🚀 Launch Demo
JLmol Application Screenshot
JLmol Desktop Application Interface

Download JLmol

Get the latest version of JLmol for your operating system. Pre-built executables are available for all major platforms.

🪟

Windows

.exe installer

Download
🍎

macOS

.dmg package

Download
🐧

Linux

.AppImage, .deb, .rpm

Download
All downloads are available on our GitHub Releases page