When working with large molecular assemblies, crystal structures, or intricate protein systems, selecting the right atoms can be surprisingly time-consuming. Graphical selection tools may work well for small molecules, but they tend to get messy when you’re dealing with thousands—or millions—of atoms. Need to isolate just the backbone? Or select all atoms on one side of a membrane? Manually clicking won’t scale. Fortunately, there’s a much faster and more powerful way: using mathematical expressions.
The Atoms Selector Extension in SAMSON lets you precisely select atoms based on position, element, residue number, charge, or any supported atom property—using a single line of code. If you’ve ever struggled to isolate the part of a structure you need, this may just change how you work.
What It Solves
Imagine you want to select all oxygen atoms within 5 Å of the origin. Or select all atoms with x-coordinate greater than 0 and not part of a water molecule. These kinds of operations can take minutes—or more—if done visually. Worse, they can be error-prone and inconsistent. The Atoms Selector Extension offers a reliable alternative.
How It Works
The extension allows you to define a logical expression that will be applied to all atoms in your document. Based on that expression, atoms are either selected or not. Variable and function names are intuitive and case-insensitive.
For example, to select all atoms with x and y coordinates greater than 0:
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(a.x > 0) and (a.y > 0) |
Want to select just the carbon and hydrogen atoms?
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(a.element=='Carbon') or (a.symbol=='H') |
Or maybe create a cylindrical cutout from a crystal structure centered at (15, 15) with a radius of 10 Å?
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((a.x-15)^2 + (a.y-15)^2) < 100 |
Why Use It?
- Speed: Select atoms in large structures in seconds.
- Precision: Define exact geometric criteria.
- No guessing: Your selection is fully reproducible and documented.
Try It Yourself
To use the Atoms Selector Extension in SAMSON:
- Install the extension from the SAMSON Connect platform if it’s not already active.
- Open your molecular document.
- Open the Atoms Selector interface and enter your expression.
You’ll see selected atoms instantly highlighted. From there, you can copy, export, modify, or further process your selection.
To learn more about the Atoms Selector Extension and see more examples and use cases (including how to create Batman’s batarang out of graphene), explore the full documentation page here: Making nano-batarangs (and more).
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.