If you’ve ever tried to move a group of atoms in your molecular model, only to realize that they’re no longer in the same geometric arrangement, you’re not alone. Many molecular modelers face this issue when managing atomic coordinates for complex systems. Whether you’re fine-tuning a ligand’s binding pose or making systematic changes across a substructure, fine control over atom positioning can save you hours of repetitive tasks. Fortunately, SAMSON’s Inspector offers a streamlined way to view and modify atomic attributes — and even apply changes collectively.
This blog post explores how to use SAMSON’s Inspector to edit atomic positions in batches, while preserving or overriding relative positions among selected atoms.
Understanding the Challenge
Imagine you’ve selected ten atoms that form a ring structure, and you want to shift them to a new location. Using the Inspector, you’re given two control options:
- Relative (checked): each atom’s movement is calculated relative to its original location, preserving geometry.
- Relative (unchecked): all selected atoms are assigned the same coordinates, collapsing them into one point.
Knowing when to use each option makes a big difference. For structural tweaks where geometry matters (e.g., functional groups, protein side chains), enabling Relative ensures spatial integrity. If you’re resetting positions entirely (e.g., placing atoms at origin for reference), disabling it might be the right move.
Step-by-Step: How to Modify Atom Positions
1. Select the Atoms: Use SAMSON’s selection tools to choose multiple atoms. You can hold Ctrl/Cmd to select more than one.
2. Open the Inspector: Go to Interface > Inspector, or press Ctrl+2 (Windows/Linux) or Cmd+2 (Mac).
3. Locate Position Attributes: In the Inspector, type position in the filter box to narrow down the list of attributes.
4. Adjust Positions: Modify the coordinate values. If Relative is active, atoms will move collectively. If you deselect it, all atoms might snap to the same coordinates, depending on your input.
Why It Matters
When setting up simulations or analyzing structural variations, the ability to apply attribute changes to multiple nodes in one go can drastically improve workflow efficiency. Manual updates through scripting or one-at-a-time adjustments can introduce inconsistencies or simply take more time than needed.
The Inspector’s behavior — applying modifications to all nodes while only displaying one node’s attributes visually — also avoids clutter, offering a cleaner interface for batch operations.
Restoring Defaults and Undoing Changes
Worried about making a mistake? Hover over an attribute’s name, and if you see a special cursor, you can double-click it to reset the value to its original state.
Also, thanks to SAMSON’s integrated history mechanism, you can always undo unwanted changes to recover previous geometry states.
Wrap-Up
For molecular modelers frequently adjusting atom positions — whether for docking, alignment, or visualization — the Inspector in SAMSON is more than just a viewer. It’s a precise editor that helps you enact consistent changes while maintaining molecular structure. And once familiar with its batch-editing and filtering functionalities, it becomes an invaluable tool in your modeling repertoire.
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.