Crystal Builder
Crystal Builder icon

Crystal Builder

A free, open-source desktop crystal structure builder for macOS, Windows and Linux. Read and write CIF, edit symmetry and bonding, build a MOF on a net, and run a force field, DFTB+, porosity or a powder refinement on the result.

Found a bug? Report it from inside the app: Help ▸ Send Feedback…

Download for macOS Apple silicon Macs (M1 and later) Latest release Intel Mac? Download the x86_64 build
Download for Windows 64-bit Windows Latest release
Download for Linux AppImage, x86_64 Latest release
New

New in 1.1

  • Carbon builders. Fullerenes, nanotubes, graphene and twisted bilayers join the disordered carbons, from 0D to 3D under Modules ▸ Carbon builder.
  • Linux. An AppImage for x86_64, with thanks to Jose Ivan.
  • Thermochemistry. Free energies, phonons, an IR spectrum and the quasi-harmonic F(V, T), under any engine.
  • Reticular design. Partitioned pores, supertetrahedra, merged nets and rod SBUs in the MOF builder.
  • The assistant's work, taken back in one click, and the assistant can now restyle a tab as well as edit it.
  • Help ▸ Check for Updates, SHELX .res files, and View ▸ Along (hkl)….

See all changes Source All releases Report an issue

Assistants

Let an AI assistant work in the window.

Crystal Builder serves its own verbs as MCP tools, and ships a skill that teaches an assistant (Claude Code, Claude Desktop, Cursor, Codex, any MCP client) to use them: open, prepare, edit, relax, measure and render, through the same commands a person's clicks push. Each change lands in your open tab as one undo step, in front of you, and its whole request can be taken back in one click.

Prompt to Claude Code

Get Ni2Cl2BTDD.cif ready for a calculation and show me the channel.

Real output. With the Crystal Builder skill, Claude Code opened the deposited CIF, read the diagnostics, ran prepare and reported each step:

  • 27 sites were symmetry copies of others: 1152 atoms written, 378 distinct
  • primitive cell of the R-centred lattice: 126 atoms
  • pore water O4, disordered across a mirror, ordered
  • 42 water molecules removed from the pores
  • 12 hydrogens on arene rings, 12 as water on the metals

Then it checked the result (one framework, C36H24Cl6N18Ni6O12, every Ni six-coordinate) and rendered it down the hexagonal axis.

You stay in charge

Two oxygens.

Every step an assistant takes is labelled as its own and grouped by the request that asked for it. The strip above the 3D view names the latest one, with Revert to take all of it back, Restore to put it back, and History for the ones before.

If you revert its work or edit in between, the assistant is told on its next call, so it looks again rather than building on a structure that is no longer there.

What it can do

  • Inspect a structure first: composition, symmetry, coordination, and coded diagnostics, each with its remedy.
  • Prepare a deposited CIF and say what every step chose.
  • Build a framework on a net, add, move and substitute atoms, recalculate bonds when asked.
  • Relax and measure: energies, pore volume and area, a PXRD pattern.
  • Restyle a tab: style, rings, Colour by, polyhedra, labels and colours.
  • Render what it made, and read the picture back.

How it connects

Switch it on under Help ▸ Connect an AI assistant…: the window serves the tools on your own computer (127.0.0.1, behind a token made for each launch). The download carries the xtal program beside the app, and xtal mcp passes an assistant's calls through to the window, or works headless when no window is open. Every step an assistant takes is logged beside the structure, in agent-session.jsonl.

Register it

The assistant page in Preferences gives the exact line for your install. With xtal on your path it is:

claude mcp add crystal-builder -- xtal mcp

xtal skill install puts the skill where Claude Code reads it.

Features

What Crystal Builder does.

Every image below is the real application with a real structure, taken by the scripts that illustrate the user manual.

A framework built on the acs net, drawn with polyhedra.

01 Build

  • Build a MOF from a net, a node and a linker. PORMAKE is built in, with its 867 building blocks and the RCSR nets, and the build reports what came out against what was asked.
  • Reticular design: partitioned pores, zeolitic supertetrahedra, merged nets and rod SBUs.
  • Build by drawing in the main window: place atoms and bonds by hand, straight into the crystal.
  • Build a molecule by drawing in a 2D sketcher.
  • Amorphous polymers packed into a box or a membrane, from the library's monomers or your own.
  • Place guest molecules into your structure.
A (10,10) nanotube with its ends capped with hydrogen.

02 Carbon

  • Fullerenes from their face spirals: every isomer up to C40, and the isolated-pentagon ones to C100.
  • Nanotubes from (n,m), periodic or with capped ends, carbon or BN.
  • Graphene of any two elements, stacked AA, AB, ABC or AA′, and twisted bilayers at a commensurate angle.
  • Disordered carbons (zeolite-templated or schwarzite) as one terminated sheet that follows a net.

03 Symmetry and bonding

  • Space groups and their subgroups, Find symmetry, Standardize, primitive and supercells, a slab along (hkl). Find symmetry names any site off its special position, and can snap it on.
  • Bonds you stay in charge of. They change only when you press Recalculate Bonds: never on load, on an edit, or after an optimisation. A bond type set by hand always wins.
  • Prepare for simulation merges duplicates, orders disorder, removes solvent and adds hydrogens, in one undo step.
  • The CIF carries the bonds, so what you save is what you reopen.
The Force Field panel after a UFF relaxation.

04 Simulate

  • Engines. UFF with UFF4MOF, xTB, DFTB+ (with band structures and densities of states), MACE, ORB-v3, and MatterSim.
  • Geometry optimizations and relaxed coordinate scans that hold a distance, angle, or cell volume.
  • Thermochemistry: free energies, phonons, an IR spectrum and the quasi-harmonic F(V, T), saying what they left out; and a bulk modulus from an equation of state.
ZIF-8 and the surface of the pores a probe can reach.

05 Pores

  • Porosity with Zeo++ or Crystal Builder's own faster grid: accessible volume, surface area, pore sizes.
  • The pores drawn where they are: the largest included sphere at its node, and the channel surface beside the number.
  • A window too close to call is flagged, never rounded open or shut.
  • The pore size distribution exports as a CSV, with its cumulative.
The refinement workbench.

06 Powder diffraction

  • A pattern from the structure, overlaid on a measured one.
  • Peak hunting, indexing, Pawley refinement, Rietveld refinement, and Rietveld with energies from the Force Field panel's engine.
  • A diffractometer's own file: .xy, .rasx, Bruker .raw, .uxd, .xrdml.
  • A TOPAS-like parameter table: tick what refines.
HKUST-1, exported as a figure.

07 Open

  • Free and open source under the MIT licence, with the full source and history on GitHub.
  • Local files, no account. Structures, runs and measurements live in a workspace folder on your computer.
  • Formats in and out. CIF with its bonds, SHELX .res in, a project that keeps the view and runs, LAMMPS data, periodic PDB, POSCAR, XYZ, and images and printable meshes.
  • A save never destroys the last good file, and an autosave is offered back after a crash.
Platform
macOS 12.3 or later (Apple silicon and Intel, separate builds), 64-bit Windows, and Linux x86_64 with glibc 2.35 or newer (Ubuntu 22.04+, Debian 12+, Fedora 36+).
Package
A DMG for macOS, a setup .exe for Windows and an AppImage for Linux, all from the latest GitHub release.
Trust
The macOS and Windows builds are not code-signed yet, so both systems warn the first time. See Install for how to answer, if you trust where you got the file.
Updates
Help ▸ Check for Updates says when a new release is out. Download it from this page and install it over the old one.
Bundled
The MOF builder, RDKit and the sketcher, the refinement workbench, the carbon and polymer builders, phonopy, and the xtal program. Zeo++, DFTB+ and xtb are found where you installed them; MACE, ORB-v3 and MatterSim run from a Python install.
License
MIT

Install

Opening it the first time.

macOS

Open the DMG and drag Crystal Builder to Applications. Pick the build that matches your Mac; About This Mac says which.

The first time, macOS says it cannot verify the developer. To open it anyway:

  1. Double-click Crystal Builder and close the warning (Done or OK).
  2. Open System Settings ▸ Privacy & Security and scroll down to Security.
  3. Next to the message about Crystal Builder, click Open Anyway, and confirm with your password.

macOS remembers the choice; after that it opens like any other app.

Still blocked? From a terminal 
xattr -dr com.apple.quarantine "/Applications/Crystal Builder.app"

Windows

Run the installer. It installs for you alone, needs no administrator rights, and works on a managed machine.

SmartScreen shows Windows protected your PC: click More info, then Run anyway.

The installer offers the .cif and .xtalproj associations; .cif is unticked, since it usually belongs to VESTA or Mercury already.

Linux

Make the AppImage executable and run it, or tick executable in its properties and double-click:

chmod +x Crystal_Builder-*.AppImage
./Crystal_Builder-*.AppImage

On Wayland it runs on XWayland, because the 3D view draws on X11 only.

Earlier builds and their release notes are on the releases page.

Support

Something not working?

Use Help ▸ Send Feedback… inside the app, or the Send feedback… button on an error box, which carries the details along. If you open a GitHub issue instead, include the app version (Help ▸ About), your operating system, and the steps that reproduce it.

Report an issue on GitHub Browse all releases Read the source