Tired of Overlapping Labels in Molecular Views? Here’s How to Move Them Precisely

When working with complex molecular models in SAMSON, clarity in presentation is essential. Whether you’re preparing visuals for a publication, teaching, or simply trying to understand your own structure, overlapping or poorly positioned labels in the Viewport can quickly lead to confusion. If you’ve ever found yourself nudging a label again and again, unsure why it’s not behaving the way you expect, you’re not alone. Fortunately, SAMSON offers multiple precise ways to reposition labels for clearer visualization.

Here’s a practical guide to help you take control of label placement in your molecular models — a small detail that can make a big difference in readability and presentation.

Why Labels Matter

In SAMSON, labels are more than decorative text — they provide crucial context and can show names, measurements, residue types, and more. By default, labels are automatically placed at the geometric center of the labeled nodes and sit flat in the Viewport’s plane. This helps keep things neat, but for publications and presentations, you often need to nudge them just right.

Option 1: Adjusting Viewport Offset in the Inspector

If you need to make small, numeric adjustments to a label’s position, the Inspector is your best friend. Follow these steps:

  1. Select the label.
  2. Open the Inspector.
  3. Adjust its Viewport offset by entering new X, Y, and Z values manually or using the arrows.

This method is ideal when precision is key and you’re aligning multiple labels systematically.

Move a label by changing its viewport offset in the Inspector

Option 2: Use the Displace Editor (Shortcut: D)

For a more hands-on approach, you can use interactive editors:

  1. Set your Selection filter to “Labels” in the left panel.
  2. Select the desired label(s) in the Viewport or Document view.
  3. Activate the Displace editor (D shortcut or select the tool from the left-side panel).
  4. Click and drag the label to reposition it directly.

This is especially convenient for visual realignments when you’re adjusting on the fly.

Move a label with the Displace editor

Option 3: Moving Labels via Document View

If you prefer working within the Document view, you can:

  1. Select the label from the hierarchy.
  2. Enable any Move Editor.
  3. Manipulate the label’s position, either interactively or using transformation tools.

This is practical when you already know exactly which label you want to edit, especially in complex documents with many overlapping elements.

Move a label with one of the Move editors

Tips to Avoid Frustration

  • Always double-check your selection filter — labels won’t be selectable in the Viewport unless the filter is set accordingly.
  • You can use Inspector to see and modify other label attributes (font, color, display radius) while you’re repositioning.
  • Screen clutter often comes from overlapping display parameters — zoom in or out to test visibility.

Fine-tuning label positions allows you to convey molecular information more clearly, reduce ambiguity, and improve the overall presentation — all while keeping your modeling workflow smooth.

Learn more in the full documentation: https://documentation.samson-connect.net/users/latest/labeling/

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

Comments are closed.