MolViewSpec animations

Animations are sequential collections of individual MolViewSpec scenes. You can combine them freely into complex stories that render scenes one-by-one. The Mol* viewer can interpolate between these states, providing you with a powerful story telling tool tailored to structural biology.

Creating snapshots

Use the builder as normal and define the desired scene. Invoke get_snapshot() to obtain a snapshot instance (in contrast to the default way of emitting the generated state description using get_state()).

snapshot1 = builder.get_snapshot(
    title="1tqn",
    description="""
### 1tqn with ligand and electron density map
- 2FO-FC at 1.5σ, blue
- FO-FC (positive) at 3σ, green
- FO-FC (negative) at -3σ, red
""",
)

A snapshot can hold additional metadata such as a custom title and description. Markup is supported.

Combining snapshots

Individual snapshots can then be combined into an animation by providing them in the desired order using the snapshots parameter. Additionally, global metadata can be added that describes shared properties of all snapshots.

states = States(snapshots=[snapshot1, snapshot2], metadata=GlobalMetadata(description="1tqn + Volume Server")).json(
    exclude_none=True, indent=2
)

The output is valid MolViewSpec JSON that can be opened in Mol. Mol will interpolate between individual substates and add smooth transitions by default. You can further customize this behavior using the transition_duration_ms and linger_duration_ms properties.