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name: molecularnodes description: "Use MolecularNodes 5.2 in a Blender 5.2 host to import, style, animate, annotate, analyze, and render molecular structures, trajectories, density maps, and ensembles with verified API and recovery guidance." disable-model-invocation: true metadata: disco-role: operating license: NOASSERTION

MolecularNodes operating skill

Use this skill when a Researcher must plan or execute a MolecularNodes workflow in Blender: install or diagnose the add-on, load a structure or trajectory, compose styles and selections, import density/STAR/CellPack data, add annotations, persist a session, or configure a reproducible scene/render.

Route by the user's next action

• Install, import, download, cache, or format diagnosis: setup-and-import
• Static molecules, styles, selections, attributes, materials, or Geometry Nodes: molecules-and-styles
• Trajectory playback, frame mapping, IMD streaming, annotations, or session recovery: trajectories-and-annotations
• EM density, STAR, CellPack, or cryo-EM map/model workflows: density-and-ensembles
• Canvas, cameras, engines, compositor, snapshots, animation, or render recovery: scene-and-rendering

Read the nearest sub-skill first; its references contain the detailed API contracts and failure matrices. Cross-cutting failures are in references/troubleshooting.md. Source version and evidence are recorded in references/repo-provenance.md; router placement is in references/repo-routing-metadata.json.

Installation and minimal verification

For a public Python inspection environment, install the package's declared Blender API extra with python -m pip install "molecularnodes[bpy]==5.2.0". For the actual desktop add-on, use Blender 5.2 Preferences → Get Extensions → Molecular Nodes. Run the bundled read-only checker before importing data:

python sub-skills/setup-and-import/scripts/check_install.py

The checker does not install, fetch, or write files. A headless bpy pass is useful for data/API checks but is not proof of the desktop extension panel, viewport, or GPU rendering.

Global operating rules

1. Confirm a Blender 5.2-compatible host (bpy.app.version) before claiming Blender object, Geometry Nodes, material, annotation, or scene behavior. Python parsing can be a preflight but is not a substitute for the host.
2. Prefer small local fixtures and cache-first/offline checks. Treat remote downloads, EMDB/PDB services, IMD servers, missing micrographs, and large renders as explicit external boundaries.
3. Preserve source paths, world scale, entity type, named attributes, selection names, node links, collection ownership, and session state when handing work between routes. Reacquire Blender references after scene reset/load.
4. Read back outputs rather than trusting a call return: object/modifier, attributes, node links, materials, frames, collections, camera settings, render files, or .MNSession state as appropriate.
5. Do not promise interactive viewport, desktop extension UI, or GPU rendering from a headless bpy import. See the nearest troubleshooting reference.
6. Never make runtime instructions depend on the original MolecularNodes checkout or private inspection environment.