Molecular modeling often involves navigating between abstract representations, such as sequences, and the tangible three-dimensional structures they correspond to. This can be disjointed: selecting residues in a sequence viewer may not reflect immediately in your 3D modeler, or vice versa. The result? Missed selections, cumbersome workflows, and difficulty identifying patterns across different levels of representation.
To address this, the Sequence View in SAMSON provides synchronized interaction between the residue-level sequence and its 3D structural counterpart. This makes sequence-based editing and visualization more connected, precise, and easy.
What is the Sequence View?
The Sequence View is an interactive panel inside SAMSON that displays the linear amino acid or nucleotide sequence of one or more chains in a structure. Crucially, this view is synced with SAMSON’s 3D Viewport and Document View:
- Click on residues in the Sequence View to select them in the 3D Viewport and vice versa.
- Selections stay consistent across views, saving time and avoiding mistakes.
This is particularly helpful for identifying and editing specific functional residues, preparing simulations, or just staying oriented while comparing different conformers or chains.
Residue Colorization: Making Biophysical Properties Visible
Another advantage of the Sequence View is that it lets users color residues based on biophysical properties—such as hydrophobicity or charge—and pushes those colorizations into the 3D Viewport. This is a simple yet powerful way of visualizing important molecular features at a glance.
Have you ever wanted to quickly color-code acidic vs. basic residues in your structure? Or identify hydrophobic patches in a large protein? A few clicks in the Sequence View, and your 3D model reflects exactly that.
By making these properties visible, you can more easily plan mutations, design ligands, or communicate your findings to collaborators without diving into scripts or adding manual annotations.
Accessing the Sequence View
You can open the Sequence View in SAMSON in two ways:
- From the Home menu, click on View sequence.
- Right-click on the structure in your Document View and select Structural model > View sequence.
Working with Multi-Chain Structures
If your structure contains multiple chains, SAMSON will prompt you to choose which sequences to view when opening the Sequence View. This keeps things tidy and ensures you’re looking at just the parts of the model that interest you.
Why It Matters
By bringing together symbolic and spatial representations in real time, the Sequence View in SAMSON helps molecular modelers work more accurately and intuitively. Less time toggling between software or guessing residue positions—and more confidence in selections, edits, and analysis.
To learn more, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.