Simplifying Molecular Annotations in SAMSON with Note Attributes

When managing complex molecular systems in SAMSON, it’s easy to feel overwhelmed by the sheer number of nodes and properties involved. An especially useful—but often overlooked—feature is the ability to annotate structures using Note nodes. These allow users to document molecular designs, workflows, or hypotheses directly within a project.

However, as your project grows, navigating these notes can become cumbersome. If you’re struggling to find specific annotations, or you’d like to sort or filter them based on logical conditions, the Note attributes in NSL (Node Specification Language) can significantly streamline your workflow.

Why Note Attributes Matter

Whether you’re building simulations, preparing a paper, or collaborating on a molecular model, being able to search and filter notes precisely means less time browsing and more time modeling.

In SAMSON, all note-specific filtering can be done using the nt namespace. Here’s a quick breakdown of useful attributes for note nodes:

Attribute	Short Name	Values	Example
hidden	h	true, false	nt.h, not nt.h
name	n	string (quoted)	nt.n "Ligand*"
selected	(none)	true, false	nt.selected, not nt.selected
selectionFlag	sf	true, false	nt.sf
visibilityFlag	vf	true, false	nt.vf false
visible	v	true, false	nt.v, not nt.v

Use Case: Instantly Finding Important Notes

Imagine you’ve annotated a few critical findings in your system as note nodes named "Ligand Binding Site A", "Ligand Binding Site B", and so on. To focus only on those, use:

This filters all note nodes whose names start with “Ligand,” helping you instantly zone in on the ones that matter.

Manage Note Visibility

Rather than toggling visibility manually, NSL lets you hide all visible notes using:

or show only those that were hidden:

Enhance Team Collaboration

Before sharing your molecular design with a team, you may want to clean up visible notes, leaving only those that are relevant for reviewers. Simple filters, such as:

can help you manage what’s selected, keeping your file lighter and better organized.

Quick Tip: Combine Filters

You can combine multiple criteria to filter even more precisely:

This shows only visible notes related to ligand binding. Handy for presentations or generating figures!

These filtering capabilities may seem minor at first glance, but they become valuable time-savers as your molecular systems increase in complexity.

To learn more about note attributes and see the full documentation, visit the official NSL note attribute documentation.

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