Molecular modelers face unique challenges when working with complex biomolecules like proteins or nucleic acids. One common issue is efficiently analyzing and interacting with sequences while keeping the structure context in mind. If you’ve ever struggled to toggle between sequence details and structural representations, SAMSON’s Sequence View feature might be the solution you’re looking for.
The Sequence View in SAMSON is an interactive tool designed to seamlessly link residue selections between different representations. Selecting residues in the Sequence View automatically selects them in both the 3D Viewport and the Document View, building a truly synchronized workflow that saves time and reduces potential errors.
But there’s more! Here are some of the key capabilities of Sequence View that can make your molecular modeling projects more efficient and intuitive:
Effortless Residue Selection and Syncing
When analyzing biomolecules, selecting specific residues or domains is a frequent task. SAMSON’s Sequence View allows you to directly select residues in the linear sequence representation. These selections are instantly mirrored in the 3D Viewport and Document View, ensuring you always have a consistent view of the molecule. Conversely, selecting residues in 3D immediately highlights the corresponding parts of the sequence—a significant improvement in interactivity.
Colorize Residues by Biophysical Properties
Ever wanted to visualize residue properties like hydrophobicity or charge directly on your molecular structure? Sequence View enables you to apply meaningful color schemes to residues based on their biophysical properties. Not only do these custom colors make sequences easier to interpret, but SAMSON also transfers this coloring to the residues in the 3D Viewport, giving you a clear structural understanding at a glance.
Accessing Sequence View in SAMSON
Accessing Sequence Views is straightforward:
- Click the View sequence command in the Home menu.
- Alternatively, right-click on a structure in the 3D Viewport, navigate to Structural model > View sequence in the context menu.
If your structure contains multiple chains, SAMSON facilitates chain-specific workflows by providing a pop-up. This allows you to select which sequence(s) you want to display. This feature is particularly useful when working with large or multi-chain macromolecular assemblies.
Applications of Sequence View
Whether you’re preparing to run a simulation, designing a mutagenesis experiment, or simply trying to understand a biomolecule better, Sequence View is an incredibly versatile tool. By bridging the gap between sequence information and 3D structural context, it makes molecular modeling workflows smoother and easier. Additionally, features like residue colorization help you communicate results effectively, improving both your analysis and presentations.
For further details, visit the official Sequence View documentation page. It offers comprehensive instructions to make the most out of this feature.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net and start exploring!