If you’ve ever tried to edit a whole group of atoms in your molecular model—maybe to reposition a residue without disturbing the relative geometry of its atoms—you might have found it tricky to avoid collapsing everything into a single point. This is a common challenge when working with atom groups in molecular modeling software. Fortunately, SAMSON offers a practical solution through its Inspector.
The Inspector in SAMSON is not only for viewing molecular properties—it’s also a tool for editing them in bulk, intelligently. One key feature is the Relative option, which helps you perform transformations on multiple nodes (like atoms) while maintaining their spatial relationships.
What’s the Problem?
Let’s say you’ve selected several atoms because you want to move a side chain or residue to a new location. When you type in a new position in the Inspector without adjusting the relative setting, all atoms may jump to the exact same coordinates, destroying the residue’s internal geometry.
This happens when the Relative option is unchecked. All selected atoms receive the same absolute value—like you’ve glued them on top of each other. Luckily, SAMSON gives you the control to avoid this.
Using the Relative Option
When you select multiple atoms in SAMSON and want to reposition them together while preserving their structure, make sure to:
- Open the Inspector using Interface > Inspector or the shortcut (Ctrl+2 on Windows/Linux or Cmd+2 on Mac).
- Look for the position attribute in the Inspector. You can filter attributes by typing “position” in the filter bar.
- Ensure the Relative checkbox is checked before editing the position.
With the Relative option checked, when you edit the position, all atoms will move relative to their current positions—preserving their internal distances. It’s like moving the group as a rigid body.
If the checkbox is unchecked, however, all selected atoms will be assigned the same absolute position; this can be useful in other contexts but will collapse the spatial structure of your group.
Undo-Friendly and Non-Destructive
Not happy with the result? SAMSON’s history mechanism lets you quickly undo the operation. This makes experimentation safe—no permanent damage if you make a mistake.
More than Just Moving Atoms
Beyond positioning, you can modify various attributes in the Inspector. Some are editable, like the element type, while others—such as atomic weight or element symbol—are set by the system. For attributes that support it, you can even reset them to their default values by double-clicking the label.
The Inspector thus becomes not just a viewer, but a contextual editor that adapts based on selection types—atom, bond, residue, and so on.
Learn more about using the Inspector in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON and get started at https://www.samson-connect.net.