For molecular modelers, finding correlations, patterns, or transitions hidden in your simulation data is central to understanding molecular systems. Yet, doing so efficiently can be challenging without the right tools. Enter SAMSON’s Custom Scatter analysis: a powerful, user-friendly tool that allows you to compare two scalar datasets and quickly reveal relationships, clusters, or transitions in your system. If you’ve ever wondered how to spot meaningful trends in your data—ranging from improving computational experiments to gaining insight into dynamic behaviors—this feature might just save you time and effort.
Why Use Custom Scatter Analysis?
The Custom Scatter plot helps you analyze scalar observables in pairs. Each point on the scatter plot represents a specific combination of values from each dataset. Whether you’re looking for correlations (one scalar increases with another), anticorrelations (one decreases as another increases), or clusters of points representing distinct states or transitions, this approach guides you toward new insights.
One key benefit of this analysis is its speed. Thanks to its intuitive design, it’s one of the fastest ways to explore relationships within user-defined spaces. For example, you might investigate how distance correlates with changes in energy, or how RMSD pairs with radius of gyration.
How to Create a Custom Scatter Plot
Adding a scatter plot in SAMSON is straightforward. Follow these steps:
- Open the Path Analyzer.
- Ensure you have two saved scalar analyses in the Analysis Tray—these will be your data sources.
- In the Observable menu, select Custom Scatter.
- Choose exactly two scalar analyses from the tray and click Add Scatter.
That’s it! The scatter plot is ready for you to start identifying relationships or patterns immediately.
Interactive Capabilities
One standout feature of this plot is its interactivity. If your two scalar datasets are frame-linked (coming from the same path), clicking on any point within the scatter plot will allow you to jump directly to the corresponding frame in your simulation. This capability means you can actively navigate your data timeline while exploring connections, helping you link numerical trends directly to molecular structures or motion frames.
Best Practices for Maximum Insight
To make the most of Custom Scatter, it’s essential to think critically about the scalar pairs you choose. Consider the scientific questions you’re tackling. For example, plot:
- Distance vs Energy to investigate thermodynamic properties.
- RMSD vs Radius of gyration to assess conformational changes.
- SASA (solvent-accessible surface area) vs Distance to study solvation effects.
Once patterns emerge, you can use these insights as a foundation for more advanced analyses. For example, scatter plots often serve as a precursor to creating a 2D density map or exploring an Energy Landscape.
Conclusion
If you’ve been struggling to uncover relationships between your observables or are looking for a quick way to analyze scalar data visually, the Custom Scatter plot in SAMSON offers an intuitive and robust solution. With its simplicity and interactive features, it bridges the gap between computational data and actionable scientific insight.
To learn more and dive deeper into the feature, visit the official documentation page: Custom Scatter Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Learn more and get your copy of SAMSON at https://www.samson-connect.net.