When working with complex molecular scenes in SAMSON, things can get cluttered fast. Molecules, annotations, trajectories, and even animations can pile up in a hurry—especially when you’re diving into systems with dozens or even hundreds of components. One common challenge modelers face is managing what is visible—and when—during an analysis or animation session.
In this post, we take a closer look at the visibilityFlag (short name: vf) and the visible (v) attributes available for animation nodes in SAMSON’s Node Specification Language (NSL). These little-known but powerful tools make it much easier to control what appears in your animations, ultimately leading to cleaner outputs and more productive design sessions.
Why visibility control matters
Animation in molecular modeling often involves focusing on specific interactions, such as ligand binding or conformational changes. In many projects, dozens of animation nodes might be added to illustrate transitions or structural events.
Without precise visibility control, your animation readers might see irrelevant frames, cluttered transitions, or things popping in and out awkwardly. Worse, you may spend time rendering animations with elements you didn’t realize were still visible.
Understanding visibilityFlag and visible
The visibilityFlag (vf) and visible (v) attributes let you filter and select animation nodes based on their visibility status:
an.vf: Reflects whether a visibility setting has been explicitly assigned to the node (true or false). Useful for checking which nodes were manually configured.an.v: Checks whether the node is currently visible (evaluates to true or false).
Both attributes can be used to filter nodes in a scene, helping you batch-edit visibility or double-check which nodes may affect your final output.
Here are some practical examples:
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// Select all animation nodes that are set to be visible an.v // Select all animation nodes that are currently invisible not an.v // Select nodes where the visibility flag has been defined (explicit control) an.vf // Select nodes with no visibility flag set (could follow default behavior) not an.vf |
This logic makes it much easier for molecular modelers to confidently prepare animations or presentations without surprises during rendering.
Quick tip: Combine visibility with other filters
You can get even more control by combining visible or visibilityFlag with other animation attributes. For example:
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// Find visible animation nodes named with "Ligand" an.v and an.n "Ligand*" |
This kind of selective querying is particularly helpful when toggling visibility programmatically or using NSL inside scripts.
Wrap-up
Mastering the visibilityFlag and visible attributes is a quick win for scientists and educators working with detailed molecular animations. With just a bit of NSL syntax, you can streamline your visualization pipeline and focus on what truly matters: the story your molecules are telling.
To learn more and explore other attributes that apply to animation nodes, visit the original documentation page on animation attributes.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.