As molecular modelers, we often use annotations—or note nodes—to clarify structures, mark regions of interest, or collaborate with others. However, in large models, these notes can become overwhelming unless we have a fast way to search, filter, and toggle their visibility. If you’ve ever struggled to manage numerous notes in your SAMSON scenes, this post is for you.
The Node Specification Language (NSL) in SAMSON provides a concise way to select and filter through different types of nodes, including notes. The attribute space specific to notes is called note or nt for short. Among the various attributes available, the visible attribute (nt.v) might be one of the most helpful for quickly decluttering your scene.
Toggle Note Visibility in a Flash
Use the nt.v attribute to filter note nodes based on their visibility. For example:
nt.v: selects all visible notes.not nt.v: selects all notes that are currently hidden.
This makes it easy to isolate the notes you care about and hide the rest. Imagine having dozens of annotations in a protein structure—you could instantly show only the ones that matter for your current analysis, uncluttering your view without deleting anything.
Difference Between visible and visibilityFlag
NSL also includes the visibilityFlag attribute (vf) that allows finer control of visibility propagation in the node hierarchy. While nt.v indicates whether a note is visible in the viewport, nt.vf controls whether the node should propagate visibility settings from parent nodes.
This distinction is powerful in structured systems. For example, hiding a group node will hide child notes only if their vf is true. You can exclude specific notes from being automatically hidden by setting their vf to false. Then filter them like this:
nt.vf false: selects all notes not obeying visibility propagation.
Streamline Communication with Named Notes
You can also filter notes based on their name (nt.n) to highlight or organize thoughts:
nt.n "Hydrophobic Region": selects notes with exact name match.nt.n "H*": selects all notes whose name starts with “H”.
So if you adopt a naming convention in your notes, you can retrieve context-specific information fast—helpful when switching between different types of analyses or tasks.
Efficient Modeling Starts with Visual Clarity
Learning how to control the visual appearance of your notes using this subset of NSL attributes (visible, visibilityFlag, name) gives you better control over your modeling workspace. Whether presenting models to colleagues or focusing on a specific area, keeping your screen relevant and clutter-free helps you work faster and more clearly.
To dive deeper into all attributes you can use for notes in SAMSON, visit the original documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.