Finding a residue in a large molecular model can be harder than it sounds. A sequence tells you where a residue sits in a chain, while the 3D structure shows where it sits in space. Switching between those views can interrupt your work—and make it easy to lose track of what you selected.
SAMSON’s Sequence View connects those two ways of looking at a structure. Select residues in the sequence and they become selected in the Document View and 3D Viewport; select them in those views and the corresponding residues are selected in the Sequence View. That shared selection gives you a practical way to move from sequence position to structural context without treating them as separate tasks.
A simple sequence-to-structure workflow
Start by opening the sequence for the structure you want to inspect. You can choose View sequence from the Home menu, or right-click the structure and choose Structural model > View sequence from the context menu.
Once the Sequence View is open, use it to locate and select residues. Then look at the Document View or 3D Viewport to see the same selection in the structure. You can also work in the opposite direction: select residues in the structure and use the Sequence View to see where they occur in the sequence.
This is useful whenever your question has both a sequence and a spatial part. For example, you may want to identify a position in a chain, then inspect where that selected residue lies in the model. Or, after selecting a region in the 3D structure, you may want to understand its place in the sequence. The synchronized selection helps maintain that connection as you move between views.
Use color to add another layer of meaning
Sequence View can colorize residues based on biophysical properties, and those colors can be transferred to residues in the 3D Viewport. This provides a way to carry a sequence-level visual cue into the structural view, where it can be considered alongside the model’s spatial arrangement.
Color is most useful when it supports a question you are already asking. Before interpreting a pattern, make sure you know which property the colors represent and which residues are involved. Then use the 3D Viewport to examine the colored residues in their structural context. The sequence and structure views offer complementary perspectives; neither replaces the need to check the other.
When the structure has multiple chains
If a structure contains multiple chains, opening its sequence brings up a dialog where you can choose which sequence or sequences to view. Take a moment to confirm your choice before proceeding. This is especially helpful when your task concerns a particular chain: keeping the relevant sequence in view can make it easier to relate residue positions to the correct part of the model.
A small habit that prevents confusion
When moving between sequence and structure, use selection as a check: select a residue in one view, then confirm that the corresponding residue is highlighted in the other. If you are working with a structure that has multiple chains, first confirm which sequence you are viewing. These quick checks help keep your interpretation anchored to the intended residue and chain.
For more details, see the Sequence View documentation. Related workflows include selecting residues and colorizing structures.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.