Mastering Visibility and Selection in Molecular Animations

Creating molecular animations can be a powerful way to communicate structural changes and dynamic behaviors of molecules. However, it can quickly become frustrating when parts of your animations are unexpectedly hidden, incorrectly selected, or not rendered as intended. This is where understanding the animation attribute space in SAMSON’s Node Specification Language (NSL) can save a lot of headaches.

In SAMSON, every animation node—a snapshot of molecular structure at a given time step—can be filtered using specific attributes defined in the animation (or an) namespace. These include visibility, selection, naming, and flag control, which persist from the more general node attribute space. Grasping how these attributes work is essential for modelers seeking precise control of their scenes.

Why Visibility and Selection Matter

Imagine you’re preparing a presentation to highlight a ligand’s interaction with its protein target. You want only the ligand and a few residues to be visible during certain frames. But when exporting the animation, unwanted atoms or structures appear, or crucial parts remain hidden. The issue likely stems from visibility and selection settings embedded in animation nodes.

Key Animation Attributes

Here’s how the NSL animation attribute space can help you:

  • Visibility: Controlled via an.v (visible), an.vf (visibilityFlag), and an.h (hidden). These let you fine-tune what’s being shown. For example, not an.v filters out all currently invisible animation nodes.
  • Selection: Toggled through an.selected and an.sf (selectionFlag). This is useful for only animating specific selections or identifying which parts of your model are active in a frame.
  • Naming: The an.n attribute allows pattern-based control. Want only frames named with an “L” prefix? Use an.n "L*" to grab them.

Best Practices

Below are practical tips to fix common issues:

  1. To display only visible parts of the animation, use: an.v
  2. To hide frames marked as hidden: not an.h
  3. To review selected frames: an.selected. In contrast to structural nodes, this attribute does not have a short form like s.
  4. Use naming conventions in your animation to simplify filtering later: an.n "A" selects nodes named “A”.

These filters can be combined to extract complex subsets of animation frames based on visibility and selection states. For example:

This gives you all visible frames that are selected and not hidden—a useful pattern when assembling educational or publication-quality animations.

Learn to Think in Filters

Ultimately, the NSL lets you think in filters: What do you want to see? What should stay hidden? What is relevant at this particular time point in your animation?

Once you integrate these NSL attributes into your workflow, you’ll spend less time chasing rendering bugs and more time refining your molecular stories.

You can explore the full list of animation-related attributes and examples in the official SAMSON documentation.

Learn more

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

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