Working with molecular animations can quickly become overwhelming within large and complex systems. Whether you’re visualizing conformational changes, analyzing dynamic interactions, or simply presenting molecular scenes, clarity is crucial. One common pain for modelers is managing what you see — and what you don’t — during animations. This is where SAMSON’s Node Specification Language (NSL) and its animation attribute space can help streamline your workflow.
The animation namespace (an) in NSL lets you filter and interact specifically with animation nodes. It inherits a number of useful attributes from the general node space, allowing you to query animation sequences based on their visibility and selection properties.
Why this matters
When you’re dealing with hundreds of trajectories or animation snapshots, trying to sort through visible and selected elements manually is not only time-consuming but prone to error. This is especially true when your animation is embedded in a larger molecular hierarchy where nodes share similar names or types.
Let’s explore a few useful attributes to help you organize your animations more effectively.
Control what you see with visible and visibilityFlag
Use an.v (an.visible) to filter animations that are currently visible in the viewport. Conversely, use not an.v to hide those nodes.
The visibilityFlag (an.vf) gives you lower-level control. Unlike visible, which reports the current visibility state including inherited visibility, visibilityFlag lets you set explicit visibility on the node itself. This is helpful if you’re scripting or building custom selection pipelines.
Query by name using partial matches
If you’re organizing animations with consistent naming patterns (e.g., “Ligand_frame_1”, “Ligand_frame_2”, etc.), use the an.n attribute:
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an.n "Ligand*" |
This will match all animation nodes whose names start with “Ligand”.
Selection tools: selected and selectionFlag
Need to identify which animation nodes are selected? Use:
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an.selected |
This is especially useful when you’re preparing scenes for presentation and want to ensure only selected conformations are displayed.
Similar to visibilityFlag, the selectionFlag (an.sf) lets you be more explicit about node selection, giving you an edge when scripting automated selections.
A practical combination
Still not convinced? Try combining filters to make highly specific queries. For instance, to find all animation nodes that are visible, named “A*”, but not selected, you could use:
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an.v and an.n "A*" and not an.selected |
This compact expression shields you from tedious mouse clicking and improves reproducibility in analysis pipelines.
Use these filters interactively in the NSL bar inside SAMSON or integrate them in scripts for a robust molecular animation workflow. They minimize the cognitive load when navigating large datasets and help you focus on what matters most: your science.
To learn more about animation attributes and their usage in SAMSON, visit the official documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.