Master Molecular Visualisations in Blender

I’ll be guiding you through a collection of eight case studies focused on creating cellular and molecular visualisations using Blender. This series is designed for complete beginners, as well as intermediate users looking to build on their existing skills. Case Study 1: Back to Basics We’ll begin by exploring the Protein Data Bank and learn how to import proteins using the Molecular Nodes addon directly into Blender. I’ll cover the basics of navigating Blender, styling proteins with Molecular Nodes, and applying simple materials and basic rendering setups. Case Study 2: Biological Assemblies We’ll step things up by working with simple biological assemblies, followed by a more complex virus structure. You’ll learn how to add RNA using the Molecular Nodes addon, explore more advanced shaders, and use additional selection tools within Molecular Nodes. Case Study 3: AI-Predicted Models Here, we’ll animate proteins and DNA—focusing on a protein with missing sections. We’ll use AI-generated models from AlphaFold and SwissModel, combine them in ChimeraX, and bring them into Blender for animation and rendering. Case Study 4: Protein Motors In this fascinating case study, we’ll animate molecular motors such as ATP synthase and E. coli flagella. I’ll guide you through an automated workflow using ChimeraX, and a manual method using Blender’s Geometry Nodes. Case Study 5: Lipid Membranes We’ll create three versions of lipid membranes: a simple model, a molecularly accurate version using data from the CHARMM-GUI database, and a dynamic version that demonstrates budding and fusion, using a specialised addon. Case Study 6: Organelles We’ll explore box-modelling techniques to create organelles that can be used alongside your close-up protein scenes. I’ll also demonstrate alternative methods for modelling Golgi apparatus membrane fusion and budding. Case Study 7: Protein Interactions We’ll explore protein–protein and enzyme interactions with chemical polymers, using small molecule models from the NIH 3D Print Exchange to help us create these interaction scenes for animation. Case Study 8: Protein Assembly and Degradation To wrap up, we’ll look at building proteins with lerping curves, and visualise protein degradation, where proteins are tagged with ubiquitin and processed by the proteasome. I hope you enjoy this journey into the molecular world through Blender, and I look forward to seeing your molecular visualisations.