A molecular group can keep roughly the same overall size while changing from compact to elongated—or back again. If you monitor only one size-related measurement, that shape change may be easy to miss. The practical question is not just “How big is this group?” but also “How spherical is it, and how does that change along the path?”
In SAMSON’s Path Analyzer, Asphericity helps answer that second question. It reports how far a selected group deviates from a spherical shape along a path or trajectory. This makes it useful when you want to track shape anisotropy rather than reduce the group’s shape to a single distance.
Why look beyond a size measurement?
A size descriptor can be useful, but it does not tell the whole shape story. Two structures may have similar overall size while differing in how their atoms are distributed. One may be more compact; another may be more stretched in some direction. Asphericity provides a complementary view by focusing on deviation from a spherical shape.
This is especially helpful when comparing structures along a path. Rather than inspecting a series of molecular snapshots one by one, you can follow a shape descriptor across the path and look for regions where the group becomes more or less spherical. The plot does not, by itself, explain which atoms moved or what caused the change. It gives you a signal to investigate alongside the structures and other measurements.
Set up the analysis
- Open Path Analyzer.
- Choose Asphericity as the observable.
- Select the path you want to examine.
- Define the atom-containing group to analyze.
- Choose Add Time Series or Add Histogram.
The group selection matters: the analysis describes the group you specify, not automatically the entire molecular system. If you are comparing results, keep the group definition consistent so that changes in the plot are not simply a consequence of analyzing different atoms.
Choose the view that fits your question
A time series follows the shape descriptor along the path. Use it when the order of structures matters—for example, when you want to see where a change occurs or whether the descriptor varies across different parts of the path. Read the horizontal progression as the path’s sequence, not necessarily as a measure of elapsed physical time.
A histogram shows the range of sampled values. It can help you see whether the path contains a narrow or broad spread of asphericity values. Since a histogram summarizes the samples rather than showing their order, it is less suited to identifying where along the path a particular value occurred. When sequence is important, use the time-series view as well.
Use it as part of a shape picture
Asphericity is most informative when treated as one piece of evidence, not a complete explanation of molecular behavior. Pair it with Radius of gyration when you also want a size-related descriptor, and with Shape parameter for another perspective on global shape changes. If the plots suggest a notable change, inspect the corresponding structures to understand what is happening in the selected group.
This combination can help avoid a common interpretation trap: treating a stable size measurement as proof that the shape is unchanged. Size and shape answer different questions. Looking at them together gives you a more useful way to describe how a group varies along a path, while still leaving structural inspection as the way to investigate the cause.
For the complete setup and details, see the Asphericity documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.