Why Your Molecular Labels Look Off — And How to Fix It

Labels are a critical part of molecular visualization — they help identify atoms, residues, molecules, and key spatial measurements. But if you’re a molecular modeler working in SAMSON and your Viewport looks cluttered or unclear, misaligned labels might be the culprit.

Default label placement in SAMSON is functional, but it doesn’t always give that extra clarity needed for figures, videos, or interactive presentations. Fortunately, SAMSON offers multiple intuitive ways to move labels to better positions. Here’s how you can take full control over label positioning for better visuals and clearer communication.

Why move labels?

By default, labels are placed at the geometric center of the nodes they describe. In many cases, that works fine. But for dense systems, overlapping elements, or when preparing publication-quality images, you might want labels to stand out more or avoid hiding parts of the structure. For example:

  • A residue label might sit right over an important hydrogen bond.
  • Multiple atom labels could cluster too closely, making them unreadable.
  • You may want to align labels along a custom axis or away from the molecular structure entirely.

Three ways to move labels in SAMSON

SAMSON provides a few methods to reposition labels flexibly:

  1. Using the Inspector panel

    Select a label and open the Inspector. You’ll find the label’s viewport offset — three numeric fields corresponding to horizontal and vertical shifts in the Viewport plane. Adjust these values to nudge the label to a better spot manually.

    Move a label by changing its viewport offset in the Inspector

  2. Using on-screen move editors

    This is often the most intuitive method. First, make sure the Selection filter is set to “Labels.” Then, activate a Move editor like the Displace editor (D shortcut). Click and drag the label interactively to reposition it in the Viewport.

    Move a label with the Displace editor

  3. Through Document view + Move editors

    Prefer structured editing? Select the label in the Document view, then activate one of the Move editors as described above. This works especially well if the label is hard to select in the 3D Viewport due to overlapping structures.

    Move a label with one of the Move editors

Best practices

  • Always double-check your Selection filter. You must set it to “Labels” to interact with them in the Viewport.
  • Use minimal displacement to ensure labels remain visually linked to what they represent.
  • If multiple labels are too close, consider color-coding or selectively hiding some labels using the Document view.

Label positioning might feel like a small detail, but it can make a big difference in how clearly your molecular design is communicated — whether in a lecture slide, a publication, or a grant proposal.

You can learn more in the official SAMSON documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.

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