Edit a group of atoms confidently without breaking their internal structure? If you’re modeling or modifying molecular systems in SAMSON, this question is probably familiar. Precise control over atom positioning can be tricky, especially when you’re dealing with groups rather than single atoms. But SAMSON provides tools to make this task both simple and safe.
The Inspector in SAMSON allows you to view and modify attributes of selected nodes — whether you’re working with atoms, residues, or any other types of nodes. One common use case is editing the position of multiple atoms at once. Done right, this can save hours. Done wrong, and your molecule may stretch or collapse in unnatural ways.
Moving atoms together: the right (and wrong) way
When multiple atoms are selected, SAMSON’s Inspector allows you to change their positions. The key detail to pay attention to is the Relative option.
If Relative is checked, adjusting the position of the selected atoms will translate them all together while preserving their spatial relationships. This is particularly useful when you want to reposition a molecule fragment without distorting its internal geometry.
If Relative is unchecked, the exact same position value will be applied to all selected atoms, collapsing them into a single point. In most modeling scenarios, that’s not what you want 😬. It can destroy the structural features of your selection in one click.
Thankfully, SAMSON has a history mechanism, so you can always undo any unwanted transformation.
Step-by-step example
- Select multiple atoms in your scene.
- Open the Inspector (Interface > Inspector or use
Ctrl+2/Cmd+2). - Find the Position attribute. You can type “position” in the filter box to locate it quickly.
- Ensure the Relative checkbox is ON.
- Change the X, Y, or Z values to move the selection while preserving its shape.
This method gives you fine control over groups of atoms and lets you reposition parts of your model with precision. When modeling large structures or making adjustments to docking configurations, moving whole segments efficiently can save you a lot of time.
A note about visual feedback
As you modify attributes, SAMSON updates the scene in real time. This immediate visual feedback helps you validate changes as you make them. If you’re unsure whether a change worked as expected, remember: undo is just a click away.
To explore other ways to use the Inspector tool and learn more about its capabilities, visit the documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.