When working with a molecular structure, it is easy to lose track of where a residue in the sequence sits in the 3D model. You may recognize a region in the sequence, then have to search the structure to find the same residues—or select atoms in 3D and wonder which part of the sequence they belong to. Switching views can interrupt your train of thought, especially when you are comparing regions or preparing a structure for downstream work.
SAMSON’s Sequence View helps bridge that gap. It is interactive and synchronized with the document: selecting residues in the sequence also selects them in the Document View and 3D Viewport, and selections made in those views are reflected back in the sequence. Instead of treating the sequence and structure as separate references, you can use them together while examining a model.
Follow a residue from sequence to structure
A practical way to use this synchronization is to begin with the view that makes the region easiest to identify. If you know the residue or region you want to inspect in the sequence, select it there and look at the corresponding selection in the 3D Viewport. If you spot a region of interest in the structure first, select it in the viewport and use the sequence view to see where that selection lies in the chain.
This two-way feedback is useful for keeping context while moving between sequence-level and structural questions. For example, you can identify a group of residues in one view, then inspect their location in another without manually recreating the selection. It can also help when explaining a model to someone else: the sequence provides a readable reference, while the 3D view shows the spatial arrangement.
Open the sequence view for the structure you need
There are two documented ways to open a Sequence View. From the Home menu, choose View sequence. Alternatively, right-click a structure and choose Structural model > View sequence from the context menu.
If the structure contains multiple chains, SAMSON presents a pop-up that lets you choose which sequence or sequences to view. This gives you a chance to focus on the chain relevant to the task, or to open more than one sequence when that is useful. Checking the chain choice before interpreting a selection can help avoid confusion when a structure contains several sequences.
Use color to make sequence patterns visible in 3D
Sequence Views can also colorize residues according to biophysical properties. Those colors can be transferred to the corresponding residues in the 3D Viewport, giving you a visual way to connect a pattern in the sequence with its location in the structure. This can be helpful when a selection alone is not enough to keep several regions distinct during inspection or presentation.
The key benefit is continuity: select in either view, check the matching context in the other, and use color when it helps make residue properties easier to follow. To explore the available controls and workflow, see the Sequence View documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.