How to Edit Atom Properties Without Breaking Your Model

Molecular modelers often need to inspect and modify properties of atoms or groups of atoms when preparing systems or analyzing simulations. However, editing atomic attributes can be risky: one wrong click and your structure may no longer make sense. Fortunately, the Inspector in SAMSON provides a well-designed, intuitive interface for safely viewing and changing atom attributes — even for large selections.

Let’s walk through how you can use the Inspector to modify properties like position, type, and more while keeping control and precision — essential skills when building or refining molecular systems.

Getting Started: Open the Inspector

First, select an atom or group of atoms. You can open the Inspector in one of three ways:

  • Interface > Inspector from the top menu
  • Shortcut: Ctrl + 2 on Windows/Linux or Cmd + 2 on macOS
  • Click the Inspector icon in the context toolbar that appears when you select an element

Understanding Node Attributes

Once a selection is made, the Inspector displays its attributes, organized by node type (e.g., Atom, Bond, Residue). Inside each type group, you’ll see clusters of related attributes, such as basic properties, position data, or rendering options.

Inspecting an atom

Some attributes are fixed — such as atomic weight, which depends on the element — but others, like element type, can be modified. For example, changing an atom from carbon to nitrogen will update all related values accordingly.

Modifying Multiple Atoms

The Inspector isn’t just for single atoms. If you select multiple atoms of the same type, you can change shared attributes all at once. A useful example is updating atom positions in bulk while controlling whether their relative positions are maintained.

Inspecting multiple atoms
Changing positions

The Relative option is crucial here:

  • If Relative is checked, all atoms move together, preserving their internal geometry.
  • If Relative is unchecked, all selected atoms are moved to the same position — likely not what you want for molecular modeling.

Good news: if you make a mistake, you can always undo your last action using SAMSON’s history panel.

Filtering Attributes

Looking for a specific attribute among many? Use the filter bar at the top of the Inspector to search, e.g., type position to bring up only position-related fields. This makes the interface much faster when working with large models or unfamiliar node types.

Filtering attributes

Try modifying a value directly in the Inspector. As you change a position coordinate, the atom’s location updates live. This kind of hands-on control helps refine geometries quickly and visually.

Changing attributes

Resetting Attributes to Default

Mistyped a value? Many attributes can be reset to their default values. Just hover over the label until the cursor changes and double-click. This handy undo feature prevents the need to reselect or manually re-input defaults.

Resetting to default

By understanding how SAMSON’s Inspector organizes and applies edits — especially to relative positioning and multi-atom selections — you can avoid errors that might otherwise derail your modeling work.

🌐 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.

Comments are closed.