Managing Visibility and Selection of Notes in SAMSON

Anyone who works regularly with molecular modeling in SAMSON will tell you: clarity and control over your models can make a big difference. As your models grow more intricate—with annotations, labels, and multiple structural elements—being able to quickly show or hide notes, or filter them based on visibility and selection, becomes essential for efficient work.

That’s where note attributes in the Node Specification Language (NSL) come in. NSL allows you to search and filter nodes, including notes, using precise logic, saving time and reducing visual clutter.

What are note attributes in SAMSON?

Note nodes are a specific type of node used to annotate molecular models. These notes may contain labels, metadata, or other types of annotations, and they can be filtered using attributes defined in the note (or nt) attribute space.

Typical pains solved by note attributes

Too many notes? Quickly hide or show based on filters like name, visibility, or selection status.
Hard to edit scenes? Select only certain notes without manually searching through the GUI.
Presentation struggle? Filter notes dynamically for clean visualizations of complex systems.

Quick Guide to Note Attributes

Here are the main note attributes you can use with nt in NSL:

Attribute	Short name	Values	Use Case
`hidden`	`h`	`true`, `false`	Filter out hidden notes: `not nt.h`
`name`	`n`	“label”	Find specific notes: `nt.n "Hydrogen*"`
`selected`	—	`true`, `false`	Select targeted notes: `nt.selected`
`selectionFlag`	`sf`	`true`, `false`	Advanced selection logic: `nt.sf false`
`visibilityFlag`	`vf`	`true`, `false`	Visibility override filters: `nt.vf`
`visible`	`v`	`true`, `false`	Show only what’s currently visible: `nt.v`

Practical Example

Suppose you have a molecular model with many annotations, but you only want to export or work with those visible on screen. You could use:

nt.v

nt.v

Or if you’re reviewing custom labels starting with ‘Ligand_’ and want to hide those:

nt.n "Ligand_*" and not nt.v

1	nt.n "Ligand_*" and not nt.v

This simple syntax saves you a lot of manual toggling, especially with repeated workflows.

Important Notes

selected is inherited from node.selected but does not support a short name.
Attributes like name, hidden, and visible are extremely useful when used in combination.

Conclusion

Effective use of note attributes in NSL can drastically reduce the friction of working with complex models in SAMSON. Whether you’re preparing for a publication, sharing visualizations, or curating your work, mastering these simple filters will help you stay focused and organize your scene with clarity.

To learn more, visit the official documentation page.

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