When working on complex molecular systems, molecular designers and modelers often need to annotate or comment their models using note nodes. These notes can be essential for keeping track of observations, hypotheses, or next steps. However, as projects grow in complexity, notes can become overwhelming and clutter the model. Fortunately, SAMSON’s Node Specification Language (NSL) provides a way to filter and manage note visibility effectively.
This blog post focuses on the note attributes available in the NSL. These attributes allow users to control which notes are visible, which are selected, and how they behave in the visual environment — improving clarity without losing information.
Understanding the nt attribute space
The nt prefix refers to the note attribute space in NSL. When you’re using NSL to search or manipulate nodes, you can specify notes using this short name. For example, to refer to visibility attributes of notes, you would use nt.v (note visibility).
Key visibility-related attributes for notes
Here are some of the most useful attributes you can use to declutter your molecular designs:
nt.hidden: Determines if a note is hidden. Set it totrueorfalse. Example:nt.hfor hidden notes.nt.visible: The inverse ofhidden. You can usenot nt.vto find all invisible notes.nt.visibilityFlag(nt.vf): Enables more nuanced control. For example, search for notes whose visibility flag isfalsewithnt.vf false.
A practical use-case: cleaning up your model view
Imagine you have dozens of notes in your protein-ligand interaction project. Some notes are for presentation, while others are technical reminders. You can use NSL to filter only the notes you want to focus on at a given moment.
For example, to display only visible notes:
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nt.v |
To hide all notes including internal comments while keeping the essential ones visible, you might want to manually tag comments meant to be hidden with specific names (e.g., “internal*”):
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not nt.n "internal*" |
Bonus: Combining filters
You can combine attributes to get refined selections. For instance, if you want to select notes that are visible and not named like “temporary*”:
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nt.v and not nt.n "temporary*" |
This approach can dramatically improve your navigation and focus during long modeling sessions.
Conclusion
The Note attributes within SAMSON’s NSL offer a precise way to control which elements clutter your visual workspace. By applying filters on visibility and naming, you reduce distractions and stay focused — especially when preparing visuals for publications or collaborators.
To learn more about note attributes and the full NSL scope, visit the original documentation page:
https://documentation.samson-connect.net/users/latest/nsl/note/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net