Making Sense of Animation Visibility in Molecular Models

When working on molecular modeling projects involving animations—whether for simulations, presentations, or collaborations with colleagues—clarity and control over what you see and what you don’t are critical. But how do you programmatically control visibility, selection, and naming of animation nodes in SAMSON?

If you’re already using the Node Specification Language (NSL) in SAMSON, there’s a dedicated animation attribute space (short name: an) designed specifically for working with animation nodes. Understanding this not only speeds up interactions with your models, but also helps avoid common frustrations like invisible nodes, unintended selections, or naming mismatches.

What’s the pain?

Let’s say you’re preparing a dynamic visualization of a ligand-protein interaction. You’ve created multiple animation nodes to represent different states. Suddenly, half your animation doesn’t show up. Or you can’t recall what name you assigned to a node. Or worse, the wrong elements are selected during export. This leads to wasted time debugging visibility issues instead of advancing your research.

The solution: Visibility & selection attributes

The animation attribute space provides short and clear commands to control node visibility, names, and selection states. Below is a summary of powerful tools at your disposal:

  • an.h – Hidden: Control whether an animation node is hidden or not. Use an.h to find hidden ones, or not an.h to find visible ones.
  • an.v – Visible: Acts like a filter: an.v selects visible animation nodes. Combine with not for invisible ones.
  • an.vf – Visibility Flag: This flag toggles whether the node should be visible. Unlike an.v, this concerns the intended rather than actual visibility.
  • an.n – Name: Search and filter animation nodes by name, allowing wildcards. For instance, an.n "Binding*" captures any animation node starting with “Binding”.
  • an.selected and an.sf – Selection Controls: Use these to programmatically filter selected or unselected animation elements.

Best practices for clean animations

Here are a few practical suggestions:

  1. Name your animation nodes consistently using an.n. This makes it easier to manipulate them in bulk later on.
  2. Toggle visibility intentionally. Use an.vf false to turn off visibility before exports or presentations if needed.
  3. Use filters and conditions with not to quickly clean or isolate parts of a complex animation sequence.

These tools aren’t just for filters—they’re for sanity. They help keep large animation workflows tidy and understandable, especially when multiple users work on the same design or when reusing previous simulations in new contexts.

Example use

Want to find all animation nodes that are currently selected but invisible? Just combine attributes:

This gives you a powerful one-liner query that saves you from manual inspection.

To explore all animation node attributes and how to integrate them in your projects, visit the full documentation here: https://documentation.samson-connect.net/users/latest/nsl/animation/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here: https://www.samson-connect.net

Comments are closed.