Keeping track of residues while analyzing complex molecular structures can be frustrating, especially when toggling between 3D models and sequence data. If you’ve ever wished you could just click on a residue in the sequence and instantly locate it in the 3D view—or vice versa—SAMSON’s Sequence View might be what you’ve been looking for.
The Sequence View in SAMSON offers a synchronized, interactive representation of the macromolecular sequence connected directly with your working model. Selecting a residue in this view automatically highlights it in the 3D Viewport and Document View, and of course, the reverse holds: selecting in the 3D view updates the Sequence View.
What Does This Solve?
If you’re working with large proteins or nucleic acids, pinpointing a specific residue based on a property or number—then remembering where it is spatially—can be a pain. Manual inspection between 3D models and sequence lists in other software takes time and introduces errors, especially when subunits are involved. By consolidating these interactions in a unified interface, Sequence View reduces the friction and helps you focus on your analysis.
How It Works
Once a structure is loaded, you can activate the Sequence View in two ways:
- From the Home menu, click View sequence.
- Alternatively, right-click on the model in the viewport, then select Structural model > View sequence from the Context menu.
Multiple Chains? No Problem
If your model contains multiple chains, SAMSON gives you the option to choose which sequences you’d like to view. A popup dialog appears, and you can select one or more chains to explore.
Color-Coding by Biophysical Properties
One especially helpful feature is residue colorization based on biophysical properties. The Sequence View allows you to assign color schemes (like charge or hydrophobicity), which synchronizes with the 3D Viewport. This visual aid is incredibly useful when examining the overall structure-function relationship of proteins or identifying clusters of similar residues.
Why This Matters
Whether you’re checking mutation sites, looking for conserved regions, or validating a structural alignment, the Sequence View makes it easier to map what you see in data onto what you see in 3D. This tight connection between sequence and structure is especially useful when dealing with homology models or when exploring chain-specific behavior in complexes.
Learn more about the Sequence View feature in SAMSON’s documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.