For molecular modelers, efficiently selecting specific atoms in complex structures is a recurring challenge. Whether it’s isolating a specific region, cutting out precise nano-structures, or focusing on atoms with certain properties, the ability to select atoms based on customizable criteria is crucial. Fortunately, the Atoms Selector Extension in SAMSON makes this task straightforward, allowing you to use mathematical expressions to define selection rules with ease.
Why use the Atoms Selector?
The Atoms Selector Extension is incredibly useful for modelers who often need to extract or focus on parts of a structure based on specific attributes. Imagine selecting atoms within a specified geometric shape, such as a sphere or cylinder, or targeting atoms with unique chemical properties. This functionality eliminates repetitive manual work and introduces high precision into atom selection tasks.
How does it work?
The Atoms Selector Extension offers a simple yet powerful interface. You only need to provide a mathematical expression that defines the selection logic. The key advantage is that this tool builds on concepts from the Simple Script Extension, meaning you can utilize predefined variables and logical expressions for atom-related properties.
For example, using the expression:
|
1 |
((a.x-15)^2 + (a.y-15)^2) < 100 |
This will select atoms within a cylinder of radius 10Å centered at (15, 15) in a quartz crystal. Variables like a.x and a.y correspond to the x and y positions of atoms, allowing you to easily specify your desired selection space.
What operators and functions can you use?
The Atoms Selector Extension supports a wide range of mathematical and logical operators. Here are some examples:
- Mathematical operators:
+, -, *, /, %, ^ - Logical operators:
and, or, not - Trigonometric functions:
sin, cos, tan - Utility functions:
abs, sqrt, floor, clamp
For a full list of operators and functions supported, check out the original documentation page linked below.
Additional keyword: all
This handy keyword allows you to select all the atoms in the active document instantly without needing to write a specific mathematical expression. It’s a great option when you simply need to toggle visibility or apply changes globally.
Why Atoms Selector is essential
Whether you’re selecting atoms to isolate a functional group, modeling nano-structures, or cutting geometric sections with precision, the Atoms Selector Extension enhances both workflow efficiency and accuracy. This extension caters to a wide range of modeling needs while remaining highly intuitive to use.
To learn more about the Atoms Selector Extension and its capabilities, visit the detailed documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON today at SAMSON Connect.