Accurately selecting residues in complex molecular systems is a common pain for molecular modelers. Working with large structures—especially proteins with multiple chains—can quickly become a tedious task when manual selection is spread across multiple interfaces. If you’ve ever found yourself repeatedly hunting for the same residues in both your 3D view and a textual representation of the molecule, you’re not alone.
SAMSON‘s Sequence View offers a way out of this loop by letting you see and interact with the molecular sequence in full synchronization with the 3D Viewport and the Document View. It’s a subtle but highly effective feature that can save time and reduce errors in residue analysis and selection.
An Integrated Selection Experience
When you click on a residue in the Sequence View, that residue is also selected in the 3D Viewport and the Document View. Likewise, selecting a residue in the 3D structure highlights it in the Sequence View. This synchronization gives you constant feedback and helps avoid situations where you’re working on the wrong chain, or worse, applying changes to an unintended region of your molecule.
Why It Matters
Imagine modifying the conformation of a domain, applying coloring for visualization, or preparing for simulation. When selections are off—even slightly—the consequences can range from wrong results to wasted hours. Whether you’re dealing with post-translational modifications, refining regions of interest, or mutating specific residues, the ability to see selections reflected in all views instantly can reduce cognitive load and streamline your workflows.
Coloring by Biophysical Properties
The Sequence View does more than just selection—it allows you to visually group residues based on biophysical properties. This visual cue makes it easier to spot patterns and analyze biochemical characteristics directly from the sequence. Better still, these colors can be transferred to the 3D Viewport, helping you maintain visual consistency.
Accessing the Sequence View: Two Quick Methods
To open the Sequence View, you can either:
- Click View sequence from the Home menu, or
- Right-click on a structure and choose Structural model > View sequence from the Context menu.
If your molecule has multiple chains, a small dialog lets you choose which chains you want to visualize. This is especially useful when exploring multimers or large complexes.
In summary, the Sequence View is a small feature with large implications. It brings clarity to structure manipulation, ensures accurate selections across multiple views, and enhances your ability to analyze complex biomolecules more effectively.
To learn more, visit the official Sequence View documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON on the official website.