When Labels Are in the Way: Tweak Their Positions in SAMSON

Anyone who works with complex molecular systems knows the visual overload that can happen when too many labels clutter up the 3D view. Labels are essential to highlight atoms, residues, or entire molecules — but depending on your current zoom level or molecular conformation, they can sometimes overlap with structures or obscure important regions of your model.

Fortunately, SAMSON gives you several intuitive options to reposition labels, making your molecular visualizations cleaner and more communicative. Here’s how you can move labels in SAMSON to improve clarity without losing context.

Why Move Labels?

  • Clarify overlapping parts of a molecular structure
  • Improve readability in presentations or screenshots
  • Fine-tune layout for publication-quality visuals
  • Avoid hiding key functional groups or binding sites

By default, SAMSON places labels at the geometric center of selected nodes and keeps them aligned with the Viewport plane. This automatic placement works well for routine tasks, but for clear annotation, manual control is a better option.

Two Ways to Reposition Labels

1. Viewport Offset in the Inspector

The most precise way to reposition a label is to edit its Viewport offset manually:

  1. Select the label
  2. Open the Inspector
  3. Adjust the Viewport offset component fields (X, Y values)

This approach lets you nudge labels pixel by pixel in the Viewport, which is especially useful for static layouts intended for export or collaboration.

Move a label by changing its viewport offset in the Inspector

2. Move Editors (e.g. Displace Editor)

Prefer something more hands-on? You can use interactive editors to drag labels directly in the Viewport:

  1. Set the Selection filter to Labels
  2. Select the label you want to move
  3. Activate a Move editor, such as the Displace editor (D shortcut)
  4. Drag the label where you want it

Make sure to reset the selection filter afterward if you plan to work with other node types.

Move a label with the Displace editor

Alternatively, labels can also be moved by selecting them via the Document view and using the same interactive Move editors:

Move a label with one of the Move editors

Additional Tips

  • Keep consistency in label placement across structures for easier comparison
  • Use larger Viewport offsets when working with zoomed-out views
  • Combine label repositioning with font size changes for added clarity

Controlling label positions can significantly enhance how you communicate your molecular systems to peers, in papers, or when building presentations. These features are especially useful for educators, researchers preparing figures, or modelers dealing with large assemblies.

To explore more about labeling in SAMSON, visit the full labeling guide at https://documentation.samson-connect.net/users/latest/labeling/.

Note: 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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