Molecular modelers often face the challenge of analyzing large datasets quickly and effectively to uncover meaningful relationships between properties. Identifying correlations, anticorrelations, or clusters can lead to groundbreaking insights, but the process isn’t always straightforward. If you’ve struggled with making sense of scalar analyses, SAMSON’s Custom Scatter feature might just be the tool you need to simplify and enhance your workflows.
With Custom Scatter, molecular modelers can visually compare two saved scalar analyses in a scatter plot, offering a straightforward way to explore relationships between variables. Here’s how you can get started and make the most of this feature in your research.
Why Use Custom Scatter?
Custom Scatter allows you to bring data to life by creating scatter plots that compare scalar analyses (e.g., distance, energy, RMSD). Each point on the scatter plot represents a paired value, helping you to instantly identify patterns, clusters, or pathways in your data. This tool is especially valuable for answering specific scientific questions like:
- How does energy correlate with distance?
- Are there clusters in Radius of Gyration vs RMSD?
- Can we see trends in SASA (Solvent Accessible Surface Area) versus distance?
Leveraging these insights can guide your decision-making process or suggest further analyses, like creating a 2D density map or analyzing energy landscapes.
Steps to Add a Custom Scatter Plot
Creating a scatter plot in SAMSON is straightforward. Follow these steps to visualize your data:
- Open the Path Analyzer.
- Make sure you have two saved scalar analyses in the Analysis Tray. You can either create new scalar analyses or reuse existing ones.
- In the observable options, choose Custom Scatter.
- Select exactly two scalar analyses in the tray.
- Click Add Scatter to generate your scatter plot.
It’s that simple! Within seconds, you’ll have a clear visual representation of your data points for further exploration.
Making the Most of the Scatter Plot
Once your scatter plot is ready, you can interact with it in several useful ways:
- If both scalar analyses come from the same path and remain frame-linked, your scatter plot can stay dynamically connected to the current frame of your simulation.
- Clicking on any point in your scatter plot will move the path to the corresponding frame, helping you combine visualization with real-time exploration of your data.
This interactive functionality enables you to pinpoint the exact frames and configurations responsible for certain trends in your data—a feature that can significantly enhance your understanding of complex molecular systems.
Pro Tip: Designing the Right Pair
To truly harness the potential of scatter plots, think carefully about the scalar analyses you pair together. Focus on combinations that address meaningful scientific questions within the context of your research. For instance, “Distance vs Energy” could reveal energetic barriers, while “RMSD vs Radius of Gyration” might identify structural clusters or transitions.
Once patterns emerge, you can take it further. Use scatter plots as a jumping-off point for more advanced visualizations, like 2D density maps or energy landscapes, both of which provide additional layers of insight.
Conclusion
Custom Scatter is a simple yet powerful feature in SAMSON that brings your data to life through intuitive scatter plots. By harnessing its interactive and visual capabilities, you can uncover hidden trends, compare properties, and make data-driven decisions with ease.
To learn more about how to use Custom Scatter, visit the official documentation page: Custom Scatter Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.