Creating and analyzing molecular animations is an essential part of many workflows in molecular modeling. Whether you’re visualizing conformational changes or simulating ligand docking, animations serve as a crucial step to understand dynamic phenomena. However, managing these animations directly in the GUI can sometimes be repetitive and error-prone — especially in complex molecular systems.
This is where the Node Specification Language (NSL), and more specifically the animation attribute space, can enhance your workflow. In this post, we’ll look at how molecular modelers can selectively query and manipulate animation nodes using NSL attributes to streamline their animation management in SAMSON.
What is the animation attribute space?
The animation attribute space, with short name an, provides a dedicated context to match only animation nodes in the scene. This means you can write targeted queries to find animations with specific names, visibility states, or selection flags — all without sifting through unrelated nodes.
Practical Scenarios for Modelers
1. Finding an animation by name
You may want to isolate a specific animation named “LoopMovement” or multiple animations with a prefix like “Ligand*”. Instead of clicking around, simply use:
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an.n "LoopMovement" |
or for multiple ones:
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an.n "Ligand*" |
This speeds things up considerably if your animation structure is large.
2. Toggling visibility programmatically
Tired of hiding and unhiding animations one by one? Use:
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an.v |
to select all visible animation nodes, or:
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not an.v |
to find all hidden ones. Combine this with selection commands to manipulate these nodes directly.
3. Selectively highlighting animations
To focus attention on a group of selected animations, use:
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an.selected |
This can be helpful when reviewing key movement stages in a conformational transition and you only wish to see the animations currently selected for playback or analysis.
4. Managing visibility and selection flags
The selectionFlag and visibilityFlag attributes (short names: sf and vf) allow finer control. For example:
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an.vf false |
finds all animations with their visibility flag unset, allowing you to tailor scene clarity before generating figures or videos.
Why this Matters
As molecular systems become increasingly complex, the ability to manage animations through searchable, scriptable criteria enhances both speed and precision. By mastering these animation attributes, users can quickly isolate animations of interest, automate common visibility operations, and focus more time on science.
To learn more, please refer to the full documentation page here: Animation attributes in the Node Specification Language.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.