Making Notes Disappear in SAMSON: A Quick Guide to the ‘visible’ and ‘hidden’ Attributes

When molecular modeling projects grow in complexity, collapsing visual clutter becomes essential. One of the simplest yet most useful tricks is managing the visibility of annotations and notes added during your exploration. SAMSON, the integrative molecular design platform, allows researchers to attach notes to molecular models, highlight regions, or convey observations. However, as work progresses, these notes can start hiding more than they reveal—visually overwhelming the scene.

Fortunately, SAMSON’s Node Specification Language (NSL) provides convenient controls for selectively managing these elements through attributes like visible and hidden. These attributes are part of the note attribute space (short name: nt) which applies specifically to note nodes.

Why Control Note Visibility?

You might want to focus on specific interactions, residues, or structures in a vast molecular system. In such cases, hiding unrelated notes helps reduce noise. Conversely, showing only specific notes can help guide a discussion or emphasize results in a presentation.

The ‘visible’ Attribute

The visible attribute (short name v) allows you to control whether a note is rendered in the viewport. This is a Boolean flag, so it accepts either true or false:

  • nt.v selects all visible notes.
  • not nt.v selects all invisible notes.

To hide all currently visible notes, you could invert their visibility using the NSL or a script:

The ‘hidden’ Attribute

Similarly, the hidden attribute (short name h) also affects whether a note is displayed. Though it may seem redundant, hidden and visible capture the same logical notion using different semantic framing. It can be helpful in scripting workflows or filtering when querying based on hiding status:

  • nt.h selects all hidden notes.
  • not nt.h selects all visible notes.

The distinction is mostly stylistic, but it gives flexibility based on how your scripting logic is stated: use nt.v if you’re thinking in terms of what’s shown, and nt.h if you’re thinking in terms of what’s hidden.

Combining with Other Filters

NSL enables you to go beyond toggling these attributes in isolation. For example, you could show visible notes with names starting with ‘L’ using:

This is very helpful when only a subset of annotations is relevant for your current task.

Best Practices

  • Use consistent naming for your notes to make filtering easier.
  • Temporarily hide notes when working on dense regions.
  • Maintain visibility control as part of your modeling pipeline.
  • Experiment with short names (nt.v, nt.h) for faster command line work.

Managing visibility well can speed up navigation, reduce distraction, and bring clarity to a complex workspace. It’s a simple tool, but for those working on large biomolecular systems or presenting findings, it’s a valuable one.

Learn more in the official documentation: https://documentation.samson-connect.net/users/latest/nsl/note/

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

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