For many molecular modelers, dealing with large biomolecular structures means switching back and forth between a sequence panel and a 3D structure. Traditional tools often separate sequence information and spatial structure into different views, leading to repetitive manual selection or confusion when trying to locate residues of interest in complex proteins or nucleic acids. If you’ve ever wanted a more integrated approach, SAMSON’s Sequence View might be worth a closer look.
What Is the Sequence View?
In SAMSON, the Sequence View is not just a static list of amino acids or nucleotides. It’s an interactive panel that’s tightly synchronized with both the hierarchical Document View and the 3D Viewport.
This means that if you select a residue in the sequence list, it immediately becomes highlighted in the 3D model — and the reverse is true too. This instantly cuts down the time it takes to find the spatial context of a residue or to jump directly to a relevant site.
Color Residues by Properties
Another way that SAMSON goes a step further is the ability to color residues based on biophysical properties. Want to quickly visualize hydrophobic regions or highlight charged residues? The coloring functionality makes it visually intuitive, and the colors propagate to the 3D viewport — providing an excellent bridge between sequence-based and spatial reasoning.
This streamlines many common workflows, such as locating active sites, checking for mutations, or communicating findings through visual cues.
Opening the Sequence View
You can activate the Sequence View in two ways:
- From the Home menu, click on View sequence:
- Or by right-clicking on a structure, then selecting Structural model > View sequence from the context menu:
Working with Multiple Chains
If your molecular system contains more than one chain, SAMSON helps manage this complexity by opening a dialog box that lets you choose which sequence(s) you want to display. This avoids flooding your view with unnecessary information and helps narrow in on the right segments.
Who Is This For?
If you are:
- Comparing mutants to wild-type structures,
- Mapping binding sites to amino acid sequences, or
- Teaching or presenting molecular structures,
… this integrated system offers a practical and visual solution.
The Sequence View in SAMSON eliminates unnecessary toggling between tabs, reinforces spatial intuition, and makes structure exploration more intuitive.
To learn more, check out the full documentation page here: https://documentation.samson-connect.net/users/latest/sequence-view/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.