When working on complex molecular systems, molecular modelers often face visual clutter—overlapping structures, excessive representations, or simply too much visual data to intuitively understand what’s happening. SAMSON, the integrative platform for molecular design, offers a practical solution to this challenge through a lesser-known, yet powerful feature: presentation node visibility filtering.
Let’s look at a common workflow. Say you’re analyzing a protein-ligand complex but only want to display a specific subset of the ligand’s visual representations for clarity. SAMSON’s Node Specification Language (NSL) allows you to dynamically control which presentation nodes—the visual elements of your system—are visible based on simple, readable expressions.
Working Within the presentation Space
All filters targeting presentation nodes reside in the presentation attribute space, abbreviated as pr. These nodes dictate what’s visible in your workspace—surfaces, ribbons, ball-and-stick displays, and more.
Control What You See with pr.v
Use the pr.v attribute to filter based on visibility. It accepts boolean values: true means visible, false means hidden. For example:
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pr.v</code> — Selects all presentation nodes that are currently visible.<br><code>not pr.v</code> — Selects all presentation nodes that are hidden. |
Perfect for removing visual noise when you’re focusing on a substructure, or simply cleaning up for a publication-quality image.
More Granular Control with pr.vf
In addition to the visible attribute, SAMSON exposes the visibilityFlag, abbreviated as pr.vf. This reflects whether a presentation node is intended to be visible, not necessarily whether it’s currently rendered. This makes it useful for scripting behaviors where visibility isn’t just a visual preference but conveys specific structural states.
Combine Visibility with Naming
Let’s say you only want to isolate presentations named with a certain prefix—presentation nodes whose name starts with “L_”, for instance—and that are visible:
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pr.v and pr.n "L_*" |
This can help when comparing multiple ligand conformations or exploring specific visual layers without toggling scenes manually.
Why This Matters
Rather than manually hiding elements one by one, NSL allows you to script visibility controls. This reduces time spent on scene setup and minimizes the chance of missing a critical visual detail, especially in dense biomolecular systems.
Presentation node selectors can be embedded in custom tools, used in selection filters, or applied manually in search panels—bringing consistency and speed to your workflow.
For a full list of attributes, the presentation space supports other useful filters like pr.hidden, pr.selected, and pr.selectionFlag. Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.