Working at the atomic scale often means navigating through an overwhelming number of atoms, chains, and residues within complex structures. A recurring pain for molecular modelers is selecting the right subset of atoms from larger structures — for analysis, editing, or visualization. The process can be tedious without a good tool that is both flexible and scriptable.
The Simple Script and Atoms Selector Extensions in SAMSON offer a programmatic and highly customizable way to select atoms based on mathematical expressions. Whether you’re identifying atoms by coordinates, charges, element type, or chain ID, you can use logical conditions and script-based expressions to make precise selections.
Why is this useful?
If you’ve ever tried to isolate atoms with specific properties or spatial configurations, you’ll appreciate the versatility of this scripting approach. Consider the following tasks that become much easier with SAMSON’s selection language:
- Selecting only hydrogen atoms:
a.symbol=='H' - Selecting atoms in the right upper quadrant:
a.x>0 and a.y>0 - Identifying aromatic atoms:
a.ar==1 - Selecting atoms within a sphere of radius 10 centered at (0, 0, 2):
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if ((a.x^2 + a.y^2 + (a.z - 2)^2) < 100) a.visibilityFlag:=1; else a.visibilityFlag:=0; |
These kinds of expressions allow you to go beyond manual selection methods and define selection logic tailored to your model or analysis.
Examples in Action
Here’s a simple use-case: selecting all atoms where the x and y coordinates are positive. This could be useful for symmetry analysis or editing only a specific quadrant.
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if (a.x > 0 and a.y > 0) n.selectionFlag:=1; else n.selectionFlag:=0; |
Another common operation is to mask or de-emphasize parts of a structure for clarity during visualization. Say you want to highlight only certain elements:
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if (a.element=='Carbon' or a.symbol=='H') n.selectionFlag:=1; else n.selectionFlag:=0; |
Want to select all atoms in a cylindrical region, perhaps to simulate a nanopore? The Atoms Selector Extension also permits expressions like this one:
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((a.x-15)^2 + (a.y-15)^2) < 100 |
This selects atoms within 10Å of (15, 15) in the xy-plane.
When Precision Matters
These scripting capabilities greatly reduce the need for manual refinement in atom selection and help ensure reproducibility — an essential feature when working in computational material science, quantum chemistry, or structural biology.
You can even automate transformations or selections based on any mathematical function. For example, setting the z-coordinate of atoms based on a sinusoidal pattern:
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a.z:=sin(a.x * pi / 12); |
This kind of control makes the scriptable approach in SAMSON particularly effective for generating surface patterns, nanoarchitectures, or testing custom modifications in molecular structures.
Learn more and explore further examples in the official documentation: https://documentation.samson-connect.net/tutorials/simple-script/making-nano-batarangs-and-more/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net