MolecularNodes is a plugin for easy visualisation of structural biology and molecular data inside of the 3D modelling and animation program Blender. It provides a method for quick 1-button import of a range of formats including downloading directly from the protein data bank, or opening molecular dynamics trajectories.
MolecularNodes is powered by two key python packages:
- Biotite which powers the majority of the file parsing and downloading from the PDB
- MDAnalysis which powers the reading of a variety of molecular dynamics topology and trajectory files.
See the youtube tutorial series which covers how to install and get started with the addon.
To install Molecular Nodes, DO NOT download this repo. Instead, navigate to the release page and download the most recent release. The current version of Molecular Nodes (2.0.X) requires Blender 3.4.
The file needs to remain zipped as
MolecularNodes_2.0.X.zip. If your browser automaticlaly unzips the file (Safari on MacOS) then re-zip the file or download with a different browser (Chrome or Firefox) and then install the.zipfile.
Inside of Blender, navigate to Edit -> Preferences and click Addons then Install and select the MolecularNodes_2.0.X.zip file. Click 'Enable' which is the tick box in the top left corner.
The MolecularNodes panel can be found under Scene Properties, where there should be a button to click to install the requried python packages.
The installation instructions for the previous version can be found here. They are similar but differ slightly to the curren installation instructions.
To contribute to the project, fork and clone the Molecular Nodes repo to your local machine. I recommend using VS Code and the Blender VS Code addon which streamlines the development process.
Once installed, you can use the Blender: Build and Start command with VS Code open in the addon directory, to start Blender with the addon built and installed. Any changes that are then made to the underlying addon code, can be quickly previewed inside of the running Blender by using the VS Code command Blender: Reload Addonds.
Once happy with your code, open a pull request to discuss and get it reviewed by others working on the project. Open a draft pull request early, or open an issue to discuss the scope and feasability of potential features.
A paper has not yet been published on the addon, but if ou use it in your academic work you can site it from Zenodo:
