Molecular modeling often requires handling complex structures like proteins, nucleic acids, or macromolecular assemblies composed of hundreds or thousands of atoms. Navigating and editing these structures without getting lost can quickly become frustrating.
One of the most useful tools in the SAMSON platform for organizing and understanding molecular structures is the Sequence View. If you’ve ever wanted to edit, select, or analyze your molecular model more intuitively — perhaps in a way that resembles reading a genetic sequence — the Sequence View is worth exploring.
What is the Sequence View?
The Sequence View in SAMSON presents molecular complexes as hierarchical sequences of groups, chains, residues, and atoms. It organizes molecules similarly to how sequences are displayed in bioinformatics viewers, making it easier to focus on specific subsections of a structure. This representation is especially helpful for proteins and nucleic acids, but it generalizes well to other macromolecules.
Why does this matter?
Without a structured view, a protein model might feel like a cloud of indistinguishable atoms. Selecting a residue or chain to apply visual styles, perform calculations, or simulate interactions can feel like looking for a needle in a haystack.
Using the Sequence View, users can:
- Quickly locate and select specific residues or chains
- Rename or annotate components
- Apply styles (e.g. coloring or representations) to specific subcomponents
- Group selections for simulations or export
How to use it
When you open a molecular structure in SAMSON, you can access the Sequence View from the interface. The sequence hierarchy is displayed in a panel that can be expanded by clicking on different levels, such as molecule → chain → residue → atom.
Here are a few examples of how it can streamline workflows:
- Editing: Need to modify a specific residue? Just locate it in the sequence and double-click.
- Visual Customization: Color a specific domain or chain to distinguish it from the rest.
- Selections: Combine the Sequence View with SAMSON’s selection tools (like the Node Specification Language) for advanced operations.
When is it especially useful?
Sequence View gets particularly powerful when working with large biomolecules. For example, in homology modeling, mutagenesis studies, or preparing structures for molecular simulations, being able to isolate and manipulate parts of a model quickly is vital. Sequence View provides a clear and logical map of your structure.
Unlike flat 3D representations, which might bury residues behind others or give them misleading spatial proximity, the Sequence View ensures you get a context-aware overview of the molecule’s building blocks.
To learn more and explore how this view integrates with other SAMSON tools, visit the official reference at SAMSON’s Sequence View documentation.
Or, browse the full reference page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at www.samson-connect.net.