Choosing What You Click: Understand Selection Filters in SAMSON

When working on molecular systems with hundreds or thousands of atoms, fast and precise selection becomes critical. Do you really want to scroll endlessly or click around trying to highlight just the residues or atoms you care about? 🧬

In SAMSON, the selection filter exists to simplify this. It’s a small dropdown menu that makes a big difference: it helps you decide what type of elements you are selecting—be it atoms, residues, or entire molecules. In dense molecular scenes, applying the right filter can save minutes or even hours per session.

What Is a Selection Filter?

The selection filter in SAMSON is a tool located in the top-right corner of the viewport. It determines the granularity of your selection. By default, it’s set to Any node, which means clicking anywhere will select whatever node type happens to be under the cursor—this could range from atoms to groups or molecules.

The selection menu in the viewport

Why It Matters

Let’s say you’re visualizing a large protein-ligand complex and want to isolate all residues in the binding site area. If the selection filter is set to “Atoms,” clicking selects individual atoms—too much detail. If it’s set to “Residues,” one click selects entire building blocks at once. No more trying to connect the dots manually.

How to Use It

  • Click the dropdown next to the selection filter in the viewport.
  • Choose the desired level: Atoms, Residues, Molecules, or even custom filters.
  • The selection editor will now only select nodes of that type.

When set to Residues, for example, any click or rectangle selection in the viewport will target only residues, and the “Select all” command will select all residues in the document.

Enhancing Workflow With Custom Filters

You can also add your own selection filters using the Node Specification Language (NSL). For example, to filter all LYS and HIS residues, use:

You can save this expression as a selection filter via the Find window (Ctrl/Cmd + F), making it instantly reusable anytime you need to target those specific residues.

Add custom selection filter

Common Use Case Scenarios

  • Atoms: Ideal for detailed edits, mutations, or charge analysis.
  • Residues: Best for selections within active sites, creating Quick Groups, or exporting sequence-based subsets.
  • Any node: Flexible but less precise—great for quick overviews, not ideal for bulk actions.

The selection filter: Residues

Advanced Tip: Using Selection Filter with Shortcuts

The selection filter also affects the behavior of rectangle and point selection tools. For example, selecting with the mouse will operate at the node level defined by the filter. You can toggle between different filters as needed by combining it with Quick Group assignments to enhance responsiveness in visual modeling.

Conclusion

If you’re finding molecular selections tedious or imprecise, take a closer look at the selection filter. Applied correctly, it’s one of the simplest ways to customize your modeling workflow in SAMSON, letting you focus more on what matters—and less on how to click it. 💻🧪

To explore more, visit the full SAMSON selection documentation.

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

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