Empowering a Community of Molecular Animators

Software such as PyMOL, ChimeraX and VMD excels at the analysis of structural data, but rendering quality remains far behind that of dedicated 3D animation programs. Blender offers physically based lighting, ray-traced rendering and a complete animation system; capabilities built for film and television that translate remarkably well to molecular science.

Until recently, using them meant exporting baked geometry, a slow process that severed the link between the 3D model and the data that produced it. Molecular Nodes closes that gap. Built on Blender’s procedural Geometry Nodes system, it imports structural data directly: .pdb, .pdbx/.cif, direct download from the wwPDB, and molecular dynamics trajectories such as GROMACS, CHARMM and LAMMPS via MDAnalysis.

Because the atomic data persists inside the scene, styles, colours and animations can be driven by chain, secondary structure, B-factor or any per-atom attribute, and trajectory frames are rebuilt on playback rather than pre-exported. This also extends to a recently developed Python API that enables scripted rendering pipelines. The more significant result has been the community. Molecular Nodes is now used by researchers, illustrators and educators worldwide, and this talk focuses on what they have made with it: figures and posters, conference talks, outreach animations and short films and the face of a billion dollar tech-bio industry.

I will present a selection of these works alongside the technical developments that enabled them, and argue that open, shareable tooling fundamentally changes the relationship between scientific data and its visual communication.

Speaker Bio

Brady started out doing his PhD in structural biology of design RNA binding proteins. Frustrated with the lack of visual fidelity in molecular software, he learnt the 3D animation software Blender, eventually creating the plug-in Molecular Nodes, which has quickly become the leading tool for molecular animation.

Brady now works freelance, creating animations for academic and industry clients and continuing to develop Molecular Nodes while creating animation tutorials in person and on YouTube and is on the MDAnalysis core development team.