molecular blender

a blender plug-in for quantum chemists

Making beautifully rendered molecular images easy!

Want to contribute? Go fork me on github! Fork me on GitHub

Blender is extremely versatile

Molecular blender is an import plugin specialized for files used in quantum chemistry:

  • .xyz (single frame and trajectory)
  • .cube (orbitals)
  • .molden (orbitals)


  • imports with sensible defaults so the first pass looks good
  • materials and properties linked to ease common transformations
  • basic styling (stick model, VDW, ball and stick, wireframe)
  • support for animations (input as multiframe .xyz files) including dynamically drawing bonds
  • find and fill in aromatic rings
  • draw spheres sitting on atoms to represent atomic charges and dynamically scale them during an animation
  • draw isosurfaces from volumetric data (.cube) or molecular orbitals (.molden)


There are two basic ways to install Molecular Blender, depending on whether you want to use the optional cython enhanced isosurface routines (highly recommended, if you’re drawing isosurfaces at all).

Using (cython compatible)

The most robust way to install is to use the included

cd /path/to/molecular/blender/repo
echo '{ "Copy Target" : "/path/to/blender/scripts/addons" }' > conf.json
python3 build --copy

For this to work, you’ll need to use python 3.7 (the same version used in Blender 2.80), and have cython installed for it.

Symlink (no cython)

If you are okay with skipping cython, you can directly symlink from the python package to the blender scripts directory. The non-cython version has all the same functionality as the cython version, but may be significantly slower for certain tasks (cython version is roughly 100 times faster at drawing orbitals from molden files).

ln -s /path/to/molecular/blender/repo/molecular_blender /path/to/blender/scripts/addons/

and then it should appear in the list of Import-Export addons that can be activated like any other addon.

User supplied addon path

On Mac OS X, the path for a user supplied addon is

/Users/<username>/Library/Application\ Support/Blender/<version>/scripts/addons

where <username> and <version> should be replaced with your username and the Blender version you are using.