One of the common pain points in molecular modeling is managing and synchronizing selections between 3D structures and the sequence data they represent. As structures become more complex with multiple chains and intricate residue interactions, staying organized while moving between sequence analysis and the 3D viewport can be cumbersome.
If you’ve found yourself struggling to locate the corresponding residue in a sequence after selecting it in 3D (or vice versa), SAMSON’s Sequence View might become an indispensable part of your workflow.
Bridging Structural and Sequence Representations
The Sequence View in SAMSON is an interactive tool designed to synchronize residue selection across views: selecting a residue in the Sequence View also selects it in the Document View and the 3D Viewport — and vice versa.
This means that whenever you’re exploring a molecular structure visually in 3D, you can instantly see where in the sequence a selected residue is located. Conversely, scanning the sequence allows you to locate and highlight the residue in its 3D context. This tight integration is particularly helpful for modeling tasks like active-site analysis, mutation tracking, or structure validation.
Flexible Ways to Access the Sequence View
You can activate the Sequence View in SAMSON in two simple ways:
- Click the View sequence command from the Home menu.
- Right-click on any structural model and select Structural model > View sequence from the Context menu.
If your structure includes multiple chains, a dialog will pop up offering you the choice of which sequence(s) to view. This allows for focused analysis of individual chains and avoids clutter when working on multi-chain systems.
Beyond Selection: Colorization by Biophysical Properties
Sequence Views are not just about selection. They also offer options to color-code residues by biophysical properties, helping users quickly visualize patterns such as hydrophobicity or charge. This colorization is also reflected in the 3D Viewport, enhancing cross-view consistency.
Colorizing sequences can be especially useful when investigating structure–function relationships, comparing homologous proteins, or assessing residue environments during design workflows.
Takeaways
Whether you are fine-tuning a computational design or preparing a presentation for collaborators, SAMSON’s synchronized Sequence View can speed up residue-level operations and improve spatial awareness between structural and sequential data. If you find yourself jumping between tools or constantly searching for residue numbers in external diagrams, this feature can bring more coherence to your modeling workflow.
For more technical details and options, 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.