When working with complex macromolecules, pinpointing specific residues in a structure isn’t always easy. As the number of chains and atoms increases in your 3D molecular model, the challenge grows: which residue is where, and how do different regions of a protein behave at a glance?
This is where the Sequence View in SAMSON can become a day-to-day tool for modelers exploring biomolecular structures. Rather than relying solely on the 3D viewport—which may quickly become visually cluttered—the Sequence View allows you to browse, select, and colorize residues in an ordered, readable interface that is tightly synced with your spatial model. Selected residues in the sequence immediately become highlighted in the 3D view and vice versa.
Color as a Communication Tool
Visualizing biophysical properties across residues—such as polarity or secondary structure—is essential for many modeling and analysis workflows. The Sequence View supports residue colorization based on these properties, simplifying interpretation and highlighting structural patterns directly within the sequence. Even better, colors applied in the Sequence View can also be mirrored in the 3D viewport:
This feature is particularly useful when producing presentation materials or simply when trying to detect and analyze functional motifs confined to specific chains or domains.
Two Ways to Access the Sequence View
Starting the Sequence View takes only a couple of clicks. From the Home menu, click on View sequence:
Alternatively, right-click on any structure and navigate to Structural model > View sequence in the context menu:
If your structure contains multiple chains, SAMSON will prompt you to choose which sequence(s) to open. This makes analysis much less error-prone when working with multi-chain complexes such as hemoglobin, membrane receptors, or protein-protein interfaces:
Streamlined Navigation Across Views
The integration between Sequence View, Document View, and the 3D Viewport improves overall workflow efficiency. Whether you’re assigning mutations, scanning for active sites, or preparing for simulations, the synchronized highlighting and intuitive interface reduce the need for back-and-forth camera adjustments or menu exploration.
The Sequence View helps bridge the gap between linear sequence data and structured 3D visualization—especially helpful when annotating residues across long chains or checking if a particular point mutation occurs in a structurally significant region.
To learn more about the Sequence View and how to incorporate it into your modeling practice, read the full official documentation here:
https://documentation.samson-connect.net/users/latest/sequence-view/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON directly from https://www.samson-connect.net.