When working with complex molecular systems, molecular modelers often face the challenge of filtering and selecting specific conformations of interest among potentially thousands of possibilities. Whether you’re analyzing simulation results, comparing docking poses, or organizing your system components, being able to identify conformations with a certain number of atoms can save a significant amount of time and prevent manual errors.
Fortunately, the Node Specification Language (NSL) in SAMSON includes a dedicated attribute space called conformation (short name: co) that helps you do exactly that.
Target conformations by size with numberOfAtoms
The numberOfAtoms attribute (short form: nat) is a powerful way to filter conformations based on their atom counts. It might seem simple at first glance, but it’s extremely useful for refining searches in dense molecular assemblies.
Let’s say you’ve imported a large biomolecular system with hundreds of conformations resulting from a simulation. You are only interested in conformations with more than 100 atoms — perhaps because smaller fragments are just solvent molecules or side chains.
To isolate those larger conformations, simply use the following query:
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co.nat > 100 |
This will match only the conformation nodes with more than 100 atoms.
Range-based filtering
Want to filter conformations based on a size range? You can do that too. Suppose you’re only interested in conformations that have between 100 and 200 atoms. NSL syntax allows you to write:
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co.nat 100:200 |
Internally, this will match all conformations whose number of atoms fall between 100 and 200 inclusive.
Combine with other attributes
You can also combine co.nat with other attributes to perform more precise searches. For example, if you want all selected conformations with more than 150 atoms:
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co.selected and co.nat > 150 |
Or using a name filter along with an atom count range:
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co.n "L*" and co.nat 120:180 |
This matches conformations whose name starts with “L” and which contain between 120 and 180 atoms.
When and why this matters
This type of filtering becomes incredibly handy when conformations represent different fragments, alternative poses, or intermediate states in your molecular project. Instead of manually guessing which conformations correspond to relevant parts of your system, you can use the numberOfAtoms attribute to automate repetitive filtering tasks and focus on the science instead.
Further Documentation
To learn more about the conformation attribute space and see additional examples, visit the official documentation page:
https://documentation.samson-connect.net/users/latest/nsl/conformation/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.