When working with molecular models that have multiple conformations, navigating and managing them efficiently becomes essential—especially when the system’s complexity grows. If you’ve ever wished for a faster way to pinpoint specific conformations within large molecular structures in SAMSON, you’re not alone.
Imagine you are working on a protein-ligand interaction, and your project has generated hundreds of conformations during a simulation or optimization. Browsing these one by one just to check which ones are within a certain size range (say, 100–200 atoms) can be time-consuming and prone to mistakes.
This is where the numberOfAtoms attribute in SAMSON’s Node Specification Language (NSL) can help.
What It Is
SAMSON’s NSL offers a simple and intuitive way to query elements in your model. The co.nat attribute allows you to filter conformations based on their atom count. This is particularly useful when you want to:
- Eliminate small or very large conformations from your selection.
- Compare structures only within a certain size range.
- Quickly assess which conformations meet criteria for further analysis.
How to Use It
The numberOfAtoms attribute belongs to the conformation space (short name: co). The syntax is straightforward and expressive:
co.nat > 100will match all conformations with more than 100 atoms.co.nat 100:200matches all conformations containing between 100 and 200 atoms.
Using these filters lets you quickly home in on exactly what you need without manually inspecting each conformation. This can speed up your workflow significantly, especially when your document has dozens—or hundreds—of conformations to review.
Combine With Other Attributes
Even better, you can combine co.nat with other available attributes for more advanced filtering. For instance:
co.nat > 100 and co.selected: Finds all selected conformations with more than 100 atoms.co.n "Ligand*" and co.nat < 50: Matches conformations whose name begins with “Ligand” and that are relatively small.
This type of filtering helps modelers keep cleaner scenes, focus on relevant parts of data, and ultimately saves significant time during iterative modeling cycles.
Why It Matters
Tasks like fragment-based drug design, conformational analysis, or trajectory evaluation can generate multiple conformations per molecule. Filtering them by atom number helps reduce clutter, but more importantly, allows you to apply computational resources and visual focus only where it truly matters—on the conformations worth analyzing.
It also aids collaboration. When working on shared models, leaving behind documents with intuitive NSL queries allows teammates to quickly understand which subset of data deserves focus.
Try It Yourself
Give the co.nat attribute a try the next time you work with conformations in SAMSON. It’s a simple trick that delivers immediate value and saves time across modeling sessions.
To learn more about conformation attributes in NSL, visit the official documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.