One of the repetitive and time-consuming tasks in molecular modeling is adjusting the positions of atoms in a structure. Whether you’re building a molecular system from scratch or making structural corrections, moving atoms individually can become a bottleneck. Fortunately, SAMSON’s Inspector offers a streamlined solution that allows you to select and modify multiple atoms at once — saving you time and reducing errors.
In this post, we’ll walk you through how to efficiently modify positions of multiple atoms using the Inspector component in SAMSON. This technique is especially useful when working with groups of atoms that need to be translated in space as a rigid body, or fine-tuned relative to one another.
1. Selecting Atoms
The first step is to select the atoms you want to move. You can learn more about selection techniques in the Selecting section of the SAMSON documentation. Once selected, open the Inspector.
The Inspector can be opened via:
- Interface > Inspector
- Shortcut: Ctrl + 2 (Windows/Linux) or Cmd + 2 (Mac)
- Right-click context toolbar
2. Modifying Position Attributes
Once your atoms are selected, use the Inspector to view and edit their position attributes. To find the position attribute quickly, type position in the Inspector’s filter box. Only the matching attributes will be displayed, making the interface cleaner and easier to navigate.
Now, try editing one of the position values. When you do this, all selected atoms will respond to the change — but there’s something important to note here:
Relative vs. Absolute Changes
In the Inspector, you have the option to keep or discard relative positions among selected atoms. If the Relative option is checked (ON), any translation you apply maintains the internal geometry of the group — this is great for moving a fragment or substructure without distorting it.
If Relative is unchecked (OFF), then all selected atoms will be moved to the exact same position — which usually causes overlap between the atoms.
This distinction is subtle but crucial for effective model manipulation.
3. Undo with Confidence
Mistakes happen, and that’s okay. ANY modification you make through the Inspector can be undone, thanks to SAMSON’s integrated history mechanism. Try things out freely — you can always step back.
Example Workflow
- Select a group of atoms — e.g., side chain residues or a ligand fragment
- Open the Inspector (Ctrl+2 / Cmd+2)
- Filter by position
- Ensure the Relative checkbox is ON
- Adjust position values to translate the entire selected group without distorting internal structure
Why It Matters
Precisely positioning groups of atoms is a frequent task in molecular modeling. Whether you’re aligning fragments, cleaning up imported structures, or designing new molecules, the ability to control multiple positions simultaneously can greatly improve productivity. The Inspector provides you with a powerful, direct way to do this — all within an organized interface.
To see more examples and details, check out the official documentation page: Inspecting in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.