One common task in molecular modeling—especially when working with large molecular datasets or complex simulations—is identifying which conformations meet certain structural criteria. For example, maybe you’re only interested in conformations that contain a large number of atoms. Manually searching through data to find them can take a lot of time and may lead to errors if done inconsistently.
If you’re using SAMSON, the integrative molecular design platform, here’s a tip that can save you that unnecessary trouble. Using the Node Specification Language (NSL), you can directly write queries that target exactly what you’re looking for.
Why This Matters
Suppose you’ve just modeled a protein-ligand complex and generated hundreds of conformations through sampling. Now, you want to filter out smaller or incomplete conformations and focus on the fully assembled ones—those with more than, say, 100 atoms. Or maybe you only care about conformations within a specific size range suitable for visualization or further calculations. The good news is that with NSL in SAMSON, there is a quick and reliable way to do this.
Meet conformation.numberOfAtoms
SAMSON allows structural filtering through attribute-based queries. If you want to filter conformations based on the number of atoms they contain, use the numberOfAtoms attribute (short name: nat), specific to the conformation attribute space.
Basic Syntax
NSL makes it straightforward:
co.nat > 100: Selects conformations that contain more than 100 atoms.co.nat 100:200: Selects conformations that contain between 100 and 200 atoms, inclusive.
Here, co refers to the conformation attribute space. You can of course mix this condition with other attributes (like selected or name) to refine the query even more.
Example Use Cases
Let’s say you ran a conformation sampling algorithm and ended up with 250 possible conformations. Now, your next step is to visualize only those large enough to be structurally interesting. Use:
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co.nat > 150 |
This quickly narrows the visualization to larger conformations without manually checking each one.
Alternatively, if your interest is more constrained—perhaps focusing on medium-sized systems for a specific simulation protocol—you could use:
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co.nat 80:120 |
Why This Can Be Useful in Practice
Molecular modelers running large simulations often deal with hundreds or thousands of molecular structures. Time spent clicking through an interface to filter or tag structures grows rapidly. Using attribute filters like co.nat helps automate your workflow, reduces manual error, and brings consistency to your analysis.
This is particularly helpful in projects involving drug discovery, peptide folding, or protein-ligand binding where fine-grained selection of conformations improves downstream simulations or visual inspection.
To learn more details about all available adjustable parameters in the conformation attribute space, visit the original documentation page here:
https://documentation.samson-connect.net/users/latest/nsl/conformation/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.