A molecular structure can look more open or compact as it moves, but visual inspection alone may not tell you whether a region has actually become more exposed to its surroundings. This is especially relevant when you are studying a binding pocket, a flexible loop, a ligand, or an interface: the change you care about may be local, subtle, or spread across many frames.
Solvent-accessible surface area (SASA) offers a way to track that exposure numerically. In SAMSON’s Path Analyzer, you can follow the SASA of an atom-containing group along a path or trajectory. The result is reported in square angstroms (A^2), making it possible to see whether the selected group’s accessible surface changes as the structure moves.
Start with the question, then choose the group
Before adding a plot, decide which part of the structure you want to understand. For example: is a pocket becoming more exposed, is a loop moving into a more buried position, or is a ligand-associated region changing during a conformational path? The group you select determines what the SASA result describes. A whole-structure measurement may not answer a question about one pocket or interface, so make the selection match the biological or modeling question.
To create the analysis, open Path Analyzer, choose SASA as the observable, select a path, and define the group. Then add either a time series or a histogram. The group must contain atoms for the analysis to run.
Use the time series to locate changes
A time-series plot shows how the selected group’s SASA varies along the path. It is useful when you want to identify where exposure changes: for instance, whether a decrease happens gradually or is concentrated in one part of the path. A large drop can indicate that surface has become buried or that the structure has become more compact. These are useful clues, but they are not interchangeable explanations. Treat the plot as a measurement of changing accessible surface, then inspect the relevant structures to understand what is happening.
Keep the selection consistent with the question you are asking. If the selected group changes, the meaning of the plotted values changes too. It can also help to relate notable rises or drops to the corresponding structures along the path, rather than interpreting a number in isolation.
Use the histogram to understand the range
A histogram answers a different question: what distribution of SASA values was sampled? It can help you see whether the selected group mostly occupies a narrow range or spans a broader range of exposure. Unlike a time series, a histogram is not the best view for locating when a change occurred along the path. Choose the view that matches your goal: time series for following changes, histogram for examining the distribution.
Pair surface area with compactness
SASA describes accessible surface, while radius of gyration provides complementary information about compactness. If you want to distinguish a change in surface exposure from a broader change in molecular compactness, consider examining both observables. A decrease in SASA alone does not establish why the surface became less accessible; the additional compactness measurement can help put that trend in context.
The practical takeaway is simple: select a meaningful atom-containing group, choose the plot that answers your question, and interpret changes as evidence about exposure—not as a complete explanation of the structural mechanism. For the full workflow and details, see the SASA documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.