As a molecular modeler, exploring correlations, clusters, or transition pathways hidden in your data can feel like searching for a needle in a haystack. But SAMSON’s Custom Scatter feature provides an efficient way to bring clarity to your analysis and visualize relationships between two saved scalar analyses. In this blog post, we’ll explore how to apply this feature and why it could simplify your molecular modeling journey.
What is a Custom Scatter Plot?
The Custom Scatter analysis is designed to compare two saved scalar analyses directly against each other. This allows you to uncover patterns such as correlations, anticorrelations, and clusters within a user-defined observable space. Imagine investigating how two key properties—like energy and distance—relate: a scatter plot gives you instant insights.
Visualizing your data in this format isn’t just aesthetic. It’s a gateway to scientific discoveries, offering a high-level way to answer real-world questions like:
- How does the energy landscape evolve as molecular transitions occur?
- What is the relationship between RMSD (Root Mean Square Deviation) and Radius of Gyration?
- Can I identify interesting clusters or transitions through quantitative comparisons?
How to Set Up a Custom Scatter Analysis
It’s surprisingly simple to create your own Custom Scatter plot. Here’s how:
- Open the Path Analyzer in SAMSON.
- Ensure you have two saved scalar analyses in the Analysis Tray. These serve as your comparison properties.
- Select Custom scatter in the Observable menu.
- Choose exactly two saved analyses in the tray for the plot.
- Click Add Scatter to generate the plot.
A key advantage is that, if the two source analyses are frame-linked, the scatter plot stays connected to your simulation frames. Clicking on a point moves the trajectory to the corresponding frame, making it incredibly easy to pinpoint specific instances in your data.
Make the Most of Custom Scatter
Here are a few tips to maximize value from scatter plots:
- Carefully choose pairs of properties that directly address your scientific questions. For instance, properties like Energy vs Distance or RMSD vs SASA offer immediate biological or chemical relevance.
- Use scatter plots as a starting point before diving into more advanced techniques like 2D density maps or energy landscapes. This step-by-step approach ensures that you grasp broader trends before specializing your analysis.
Final Thoughts
The Custom Scatter feature is an accessible yet powerful way to explore potential relationships between selected properties in molecular modeling. The ability to identify correlations, highlight transitions, or zoom into specific frames ensures that your analysis remains both qualitative and actionable.
To dive deeper into the details of this feature, visit the official documentation page on Custom Scatter.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON today at https://www.samson-connect.net.