For molecular modelers, working between different representations of a biomolecule—3D structures, sequence data, and document-based views—can often lead to frustrating disconnects. You spot something interesting in a protein’s sequence, but selecting it in the sequence doesn’t highlight it in the 3D model. Or you’re zoomed in on a specific residue in the 3D viewport, but can’t find where exactly it is in the full sequence. Sound familiar?
The Sequence View in SAMSON offers an intuitive solution. This feature connects your molecule’s sequence to both the Document View and the 3D Viewport—so when you select a residue in one view, it’s automatically highlighted in the others. It’s a small change that makes a big difference in how fluidly you can analyze complex structures.
Why this matters
In multi-chain or multi-component biomolecular systems, clarity can quickly erode. Biophysicists, structural biologists, and modelers often find themselves cross-referencing between PDB files, spreadsheets, and rendered structures to track functional sites, mutations, or interactions. The Sequence View in SAMSON eliminates that friction.
Here’s what you can do at a glance:
- Visually explore the full sequence of a biomolecule
- Click on a residue in the sequence to highlight it in the 3D model and document tree
- Use colorization options to tag residues by property, then push those colors to the 3D model
Two simple access points
You can access Sequence Views in two quick ways:
- Via the Home menu by clicking View sequence
- By right-clicking on a structure and choosing Structural model > View sequence
Handling multi-chain structures
If your structure contains multiple chains, SAMSON helps you manage complexity by letting you choose which chains to visualize in the Sequence View. A pop-up dialog lets you fine-tune your selection.
The Sequence View is particularly helpful when identifying domains, motifs, or mutations across chains. For visualization, analysis, or presentation, linked views reduce the chance of context loss, helping you stay focused on the science.
To learn more about how to use the Sequence View and explore additional options, visit the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.