Understanding Relative Positioning in SAMSON’s Inspector

For many molecular modelers, adjusting the position of multiple atoms simultaneously is a common need — whether you’re setting up a complex structure, refining a model, or exploring conformational changes. But moving multiple nodes in 3D space without breaking the internal geometry of your molecule can be tricky.

This is where the Inspector tool in SAMSON helps, particularly with its Relative option when editing attributes. Knowing exactly how the Relative checkbox affects multi-selection edits will help you make cleaner, more accurate structural adjustments.

What Does “Relative” Mean in This Context?

When you select multiple atoms and try to edit their positions using the Inspector, SAMSON offers a choice: maintain their spatial relationships (relative positions) or not.

  • Relative option ON: each selected atom moves according to its current offset from the new value you enter. This preserves how the atoms are spaced relative to each other — essentially, the group translates as a whole.
  • Relative option OFF: all selected atoms are moved to exactly the same new coordinate. This can significantly alter the molecular structure — useful in some cases, but potentially destructive if done accidentally.

This behavior is subtle but important, and misunderstanding it can lead to hours of cleanup. Let’s take a closer look using visuals from the SAMSON documentation.

Case Study: Moving a Group with Relative Positioning

If you select a group of atoms and move their positions with the Relative option enabled, the whole group shifts while preserving molecular geometry. As shown below, the atoms are moved collectively without changing their mutual distances:

Inspecting multiple atoms

Inspecting multiple atoms: change positions

Now try disabling the Relative checkbox and applying a new position. All atoms assume exactly the same new coordinate, and your molecule may collapse into a single point — not what you expected.

Tips to Avoid Mistakes

  • Always verify the Relative checkbox status before editing coordinates.
  • If something goes wrong, SAMSON includes a robust undo system — use it to revert changes instead of starting over.
  • Filtering for specific attributes like position in the Inspector helps you focus only on what you want to change.

Filtering attributes

Common Use Cases

  • Adjusting ligand positions: move ligands as a block while leaving other parts static.
  • Refining a selection: nudge small groups of atoms into better spatial alignment.
  • Educational tools: demonstrate effects of rigid vs. non-rigid transformations in molecular teaching.

This feature may feel minor, but it can greatly impact your modeling effectiveness. Once you master the Relative toggle, you’ll find your atom edits are more accurate and faster.

To learn more about inspecting and editing in SAMSON, visit the full documentation: https://documentation.samson-connect.net/users/latest/inspecting/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.

Comments are closed.