Installation

To install molecular nodes, download the latest release from the github releases page. Ensure that you have a version of Molecular Nodes that matches the version of Blender you have installed.

Blender Version 3.4

Molecular Nodes 2.0 is only compatible with Blender 3.4 & above.

There are earlier versions of MN which are compatible with earlier versions of Blender, but these are no longer being developed or maintained and it is highly recommended that you use the most recent Blender and Molecular Nodes.

Details for each release are available on the releases page.

Downloading Requirements

  1. Download and install Blender 3.4 from blender.org.

  2. Download the latest MolecularNodes from the MolecularNodes Releases Page.

Download the Right Thing

Importantly do not download the entire MolecularNodes GitHub repo and try to install that. Download the bundled release from the release page and install that with Blender.

Installing the Addon

Open a New Session of Blender

Administrator

If you are on Windows, you may need to run Blender as Administrator to install additional dependencies successfully.

Open Preferences Panel

Click ‘Edit’ -> ‘Preferences’ or press Cmd + , on Mac.

Click ‘Install’ on the Addon Page

Click on the ‘Add-ons` tab on the middle left, then the ’Install’ button on the top right.

Select MolecularNodes_X.zip

The X’s will be the current version number of the add-on.

.zip Files

When downloading on MacOS with Safari, it automatically unzips the file into a MolecularNodes folder. This is extremely unhelpful as Blender requires the .zip file to install the addon. Either download with a different browser, or compress the folder again to MolecularNodes.zip.

Enable the Add-on

If the preferences panel doesn’t automatically show the installed add-on, search for the add-on to find it. Tick the box in the upper-left corner to enable it.

The nodes are now enabled and available inside of Geometry Nodes in Blender. However to be able to download and parse structure files, additional python libraries will need to be installed via pip in the next step.

Installing Biotite & MDAnalysis

There are two additional python packages which are required for MolecularNodes to function.

Biotite handles the majority of the structure file parsing. MDAnalysis handles the reading of molecular dynamics trajectories.

To install both packages, it should be a single button press inside of Blender, unless you are on an M1 or M2 Mac.

Click the ‘Install Packages’ button in the Molecular Nodes tab, which is under the ‘Scene Properties’ Tab.

MacOS M1 & M2

The ARM bundle for Blender is missing some python.h headers and is thus unable to install and compile SciPy and a number of other packages that are required for install.

Unfortunately you won’t be able to install the python pacakges by simply clicking the button.

The current fix is to create and link a separate python installation that is able to compile the packages correctly discussed here.

Run this script in your terminal, after installing miniconda

conda create --name blender python==3.10 biotite==0.35.0 mdanalysis==2.2.0 -c conda-forge -y
CONDAENV=$(conda info --envs | grep blender | awk -F ' ' '{print $2}')
mv /Applications/Blender.app/Contents/Resources/3.4/python old_python
ln -s $CONDAENV /Applications/Blender.app/Contents/Resources/3.4/python

Or do each step individually

  1. Install miniconda
  2. Create a python environment specifically for MolecularNodes
conda create -n molnodes python==3.10 biotite==0.35.0 mdanalysis==2.2.0 -c conda-forge -y
  1. Backup Blender’s current python packages.
mv /Applications/Blender.app/Contents/Resources/3.4/python /Applications/Blender.app/Contents/Resources/3.4/old_python
  1. Create a link between the installed conda environment and Blender
ln -s /path/to/miniconda/python /Applications/Blender.app/Contents/Resources/3.4/python