For molecular modelers, understanding the relationships between different variables within a molecular system is critical. Whether you’re investigating correlations between energy and distance, identifying clusters, or visualizing transition pathways, a versatile and efficient tool is indispensable. This is where SAMSON’s Custom Scatter analysis shines.
The Custom Scatter analysis feature provides a direct way to compare two scalar analyses side-by-side. By presenting this data on a scatter plot, you can detect correlations, anticorrelations, clusters, or even transition pathways within a user-defined space. This blog post will guide you through leveraging this feature to derive meaningful insights from your data.
Why Use Custom Scatter Analysis?
Custom scatter plots can simplify complex patterns, especially when working with scalar analyses. For example, discovering relationships such as Distance vs Energy or RMSD vs Radius of gyration can lead to a deeper understanding of molecular systems. The ability to assess these variables visually can save time and streamline your decision-making process.
This analysis is particularly effective for highlighting invisible trends and can serve as a foundation for more advanced techniques like 2D density maps or energy landscapes.
Steps to Add a Custom Scatter Plot
Here’s how you can quickly set up and use the Custom Scatter feature:
- Open the Path Analyzer in SAMSON.
- Create or reuse two saved scalar analyses in the Analysis Tray. These scalar analyses are the foundation of your scatter plot.
- Select Custom Scatter under the Observable options.
- Choose exactly two saved scalar analyses from the tray.
- Click the Add Scatter button to generate your plot.
What to Expect in the Visualization
After following the above steps, your scatter plot will display pairs of scalar values as points. For example, identifying clusters of similar data points or observing linear correlations becomes straightforward. The scatter plot is an interactive tool, and if the analyses are frame-linked (both derived from the same path), clicking on a specific point will move the path to its corresponding frame. This interaction increases the efficiency of exploring molecular behaviors.
Pro Tip
If you’re wondering how to get the most out of the Custom Scatter feature, start by using it with pairs that address specific scientific questions. Here are some ideas to kickstart your explorations:
- Energy vs Distance
- RMSD vs Radius of gyration
- Solvent Accessible Surface Area (SASA) vs Distance
By identifying meaningful pairs, you’ll be able to make informed decisions and take steps towards advanced analyses such as creating density maps or visualizing complex energy landscapes.
Curious to Learn More?
The official documentation page offers a comprehensive overview of the Custom Scatter analysis feature, including additional input details and interaction benefits. If uncovering molecular patterns excites you, this is a tool you’ll want to add to your workflow.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download and start exploring SAMSON at https://www.samson-connect.net.