When working with complex molecular models involving multiple animations, clarity often becomes the first casualty. Every molecular modeler has experienced the frustration of an overcrowded scene—dozens of animations running simultaneously, obscuring the very phenomenon you’re trying to observe or demonstrate.
Fortunately, SAMSON offers built-in tools to solve this. Specifically, the visible (an.v) and visibilityFlag (an.vf) attributes in the Node Specification Language (NSL) allow you to tune in exactly what you need to see, and nothing more.
What Are Visibility Attributes?
When filtering animation nodes, visibility attributes enable the selection or exclusion of animations based on whether they are currently displayed in the viewport. There are two important attributes here:
an.v: The actual visibility of an animation node. A boolean value (trueorfalse).an.vf: The visibility flag of the animation node. This is like a switch you control to decide whether the node is globally allowed to be visible.
These two work together. For instance, even if an.vf is true, an.v might still be false depending on the node’s placement in the scene or other inherited visibility states.
Use Cases: Why Should You Care?
If you’re running an animation to show ligand binding while also tracking backbone motion, you might want to hide unrelated signals like other molecular interactions or annotations. With NSL, this becomes as simple as filtering with:
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an.v |
This will filter all currently visible animation nodes—so if you only want to export or operate on what’s actively shown on screen, this is ideal.
Alternatively, to find everything that has the visibility flag set (regardless of whether it’s currently visible):
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an.vf |
You can also use negations to isolate hidden elements:
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not an.v |
This can be quite useful when cleaning or organizing your document before publication or team collaboration. By identifying hidden animations, you can delete obsolete nodes or bring important ones back into view.
Combining Filters
The real strength of NSL is composability. Visibility attributes can be combined with others like an.name or an.selected. For instance, if you want to find all visible animations related to a ligand:
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an.v and an.n "Ligand*" |
This makes your queries highly targeted and ensures you only work with relevant visual data.
How This Helps
By using visibility filters well, you can:
- Simplify your visual presentations
- Focus computational resources on what matters
- Improve model readability, especially when sharing files
- Export only the data that’s actually relevant
In short, leveraging an.v and an.vf will help you tame the visual clutter that often comes with large-scale simulations.
Want to explore more attributes and refine your molecular animations? Visit the official documentation page: Full documentation on animation attributes.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.