Finding a residue in a long molecular structure can be surprisingly disorienting. You may know its position in the sequence but not where it sits in the 3D model—or spot it in the viewport and then need to identify it in the sequence. Switching between those views can interrupt analysis and make it harder to stay oriented.
SAMSON’s Sequence View helps connect those two perspectives. It stays in sync with the document: selecting residues in the sequence selects them in the Document View and the 3D Viewport, and selecting residues in the document or viewport also updates the sequence selection. Instead of treating the sequence and structure as separate places to search, you can use either one to locate and inspect residues.
Start from the view that suits your task
If you are working from a sequence, open Sequence View and select the residues you want to examine. Their corresponding selection appears in the document and 3D viewport, helping you connect sequence position with structural context. If you are already looking at a region in the 3D model, select residues there and use the sequence view to see where they belong in the chain.
This two-way connection is useful when moving between questions such as “Which part of the sequence am I looking at?” and “Where is this residue in the structure?” It also provides a practical way to carry a selection into other structure workflows: make the selection in the view where it is easiest to identify, then continue working with that selected region.
Use color to make patterns easier to scan
Selection is useful for locating a particular region, but color can help when you want to compare properties across a sequence. Sequence Views can colorize residues according to biophysical properties, and those colors can be transferred to the corresponding residues in the 3D Viewport. This lets you inspect a property in the sequence and then see how its colored pattern is arranged in the structure.
A simple way to use this is to begin with the question you want to answer. If you need to trace a specific residue or region, use selection. If you want to scan a sequence for a property-based pattern and relate it to the model, use colorization and transfer the colors to the viewport. The sequence and 3D views then provide complementary ways to interpret the same residues.
Open the sequence for a structure
There are two documented ways to open Sequence View. From the Home menu, choose View sequence. Or right-click a structure and choose Structural model > View sequence from the context menu.
For a structure with multiple chains, SAMSON displays a pop-up so you can choose which sequence or sequences to view. This is a useful moment to confirm that you are opening the chain relevant to your task, rather than assuming a multi-chain structure has only one sequence to inspect.
A small workflow that prevents context switching
- Open Sequence View from the Home menu or the structure’s context menu.
- If prompted, choose the chain or chains you want to inspect.
- Select residues in whichever view makes them easiest to find: sequence, Document View, or 3D Viewport.
- Use the synchronized selection to check the corresponding region in the other views.
- When a property pattern is more useful than a single selection, colorize the sequence and transfer the colors to the 3D structure.
The main benefit is continuity: you can move from sequence-level identification to structural inspection without losing track of which residues you are working with. To learn more, see the SAMSON Sequence View documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.