Selecting specific atoms in large molecular systems can be time-consuming and error-prone—especially when working with complex structures like proteins, nucleic acids, or crystalline materials. If you’re a molecular modeler frustrated with manual selection tools or the limited filtering options in typical visualization software, there’s a streamlined alternative in SAMSON: the Atoms Selector Extension.
Instead of clicking through atoms one by one or guessing around graphical tools, you can now use precise mathematical expressions to define which atoms are selected in your molecular model. It’s a flexible approach that can save time and increase accuracy in your workflow—whether you’re analyzing simulation results, building structures, or designing nanomaterials.
How It Works
The Atoms Selector Extension allows you to define logical conditions involving atomic properties like position, element, chain ID, and much more. Once the condition is entered, all atoms satisfying it are automatically selected in the active document.
The syntax is the same as in SAMSON’s Simple Script Extension, with access to variables such as a.x, a.y, a.z, a.elementID, a.symbol, and more. Logical, comparison, and mathematical operators are fully supported, which means even complex logical statements can be expressed cleanly in one line.
Example: Cut a Cylinder from Quartz
Suppose you have a quartz structure, and you want to isolate a cylindrical region of 10 Å radius centered around (15,15). Typing the expression below into the Atoms Selector Extension will automatically do just that:
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1 |
((a.x - 15)^2 + (a.y - 15)^2) < 100 |
This selects all atoms that fall within that cylindrical constraint. No manual box-drawing, no guesswork—just a clean selection based on mathematical geometry.
Why Modelers Use It
- Speed: Quickly isolate regions of interest in large systems without visually scanning the structure.
- Reproducibility: Store selection formulas to re-apply them across models with similar geometries.
- Precision: Select atoms exactly based on numeric criteria—perfect for scripting repetitive tasks or standardizing workflows.
The Atoms Selector Extension also supports keywords like all if you simply want to select everything. And if you’re already familiar with using mathematical expressions for filtering, integration into your daily modeling work will be seamless.
To learn more about atom selection, scripting options, and examples like cutting cylinders or creating nano-batarangs from graphene, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.