Quickly Hide or Highlight Notes in SAMSON Using NSL

Molecular modelers often need to annotate their models with relevant information, whether it’s a hypothesis, an observation, or an explanation. These annotations are often added as notes in SAMSON, the integrative platform for molecular design. But as the complexity of a model increases, notes can start to clutter the workspace, or become difficult to manage when selectively visualizing certain parts of a system.

Fortunately, SAMSON’s Node Specification Language (NSL) provides a simple solution to this problem through the use of note attributes. With a few intuitive expressions, you can hide, show, or select only the notes you need—making your workflow cleaner and more efficient.

Why manage note attributes?

Here are a few scenarios where managing your notes can save serious time and help you stay organized:

• Focusing only on specific hypotheses while presenting a model to colleagues.
• Temporarily hiding irrelevant notes while refining a structure.
• Automatically selecting notes based on name patterns (e.g., all notes starting with “Hydrogen bond”).

By understanding how to use the nt attribute space, you can apply logical expressions to manipulate your notes quickly within SAMSON’s search bar.

Working with note attributes

Note attributes belong to the nt (short for “note”) attribute space in NSL. Here are some of the most commonly used attributes:

Attribute	Short Name	Example
hidden	h	nt.h or not nt.h
name	n	nt.n "Important note" or nt.n "H*"
selected	(no short name)	nt.selected or not nt.selected
selectionFlag	sf	nt.sf or nt.sf false
visibilityFlag	vf	nt.vf or nt.vf false
visible	v	nt.v or not nt.v

Practical examples

If you want to select all visible notes, simply type:

To hide all notes that start with the letter “L” in their name:

Selecting notes that are currently flagged for selection (useful for automation or scripting):

And to find all notes that are not currently visible:

Why it matters

These features make it easier to manage visual clutter while working on large or detailed molecular models. By combining NSL expressions, users can perform complex queries that target only the notes of interest, without manually searching through the model tree or toggling visibility per item.

This isn’t just about saving time—it’s about staying focused and making sure that your annotations serve their purpose without getting in the way.

To learn more about working with note attributes and NSL, visit the official SAMSON documentation page on NSL Note attributes.

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