Finding a residue in a protein sequence is only half the task. A modeler also needs to understand where that residue sits in the structure—and to keep the sequence and 3D views aligned while inspecting a model. Switching between separate representations can make it easy to lose track of what is selected. SAMSON’s Sequence View addresses this by synchronizing selection between the sequence, the Document View, and the 3D Viewport.
Use the sequence to find the structural context
When residues are selected in the Sequence View, the corresponding residues become selected in the Document View and the 3D Viewport. The synchronization also works in the opposite direction: selecting residues in the document or 3D representation is reflected in the sequence. This shared selection gives you a practical way to move between a residue’s place in the sequence and its position in the model without treating them as separate tasks.
For example, when you are examining a region of interest, begin with the sequence if that is where you know the residues you want to inspect. Select them there, then look at the corresponding selection in the 3D Viewport to see their structural context. If you notice a region while exploring the structure instead, select it in the 3D Viewport and use the sequence view to identify where it falls in the chain. The point is not to replace either view: it is to keep both useful perspectives connected.
Open the right sequence view
You can open a Sequence View from the Home menu by choosing 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 so you can choose which sequence or sequences to view. Taking a moment to make that choice helps keep your sequence inspection focused on the chain you intend to work with.
Use color as an additional cue
Sequence Views can colorize residues according to biophysical properties, and those colors can be transferred to the corresponding residues in the 3D Viewport. This can help you relate a sequence-based color pattern to the arrangement of residues in the model. Color is an additional visual cue, not a substitute for selection: use the synchronized selection to identify the residues you are following, and colorization to make patterns easier to notice.
A simple way to work across representations
When you need to move between sequence and structure, try this order: open the sequence for the relevant structural model; choose the chain or chains you want to view if prompted; select residues in whichever representation is most convenient; and inspect the synchronized selection in the other views. If colorization is useful for your task, apply it as a further visual aid and transfer the colors to the 3D representation.
This workflow is useful whenever the question involves both residue identity and spatial context. It reduces the mental bookkeeping of remembering which part of the sequence corresponds to a visible region, while leaving you free to start from either the sequence or the structure.
For details, see the Sequence View documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.