When working with large molecular models, it’s easy to get overwhelmed by the number of structural groups. Every atom, bond, and group adds to the visual and computational complexity. Sometimes, you just need to focus on the parts of your system that matter for your analysis — such as functional groups with specific charges.
One powerful way to simplify your model is to filter structural groups based on their partial charge. In SAMSON, this can be done using the Node Specification Language (NSL), allowing you to isolate and manipulate molecular components matching specific charge criteria.
Why filter by partial charge?
In modeling workflows, partial charge plays a critical role in non-covalent interaction patterns, molecular docking, electrostatics, and reactivity. If you’re visualizing electrostatic potentials or selecting regions of a molecule for further simulation, targeting groups with certain partial charges gives you more control and focus.
For example, positively charged groups might interact with negatively charged surfaces; selectively hiding or highlighting such domains helps sharpen the model’s relevance without the clutter of neutral areas.
How to use NSL with partialCharge
The partialCharge attribute is specific to the structuralGroup attribute space (short name: sg). You can use it to write queries like:
sg.pc > 1.5— this matches structural groups with partial charges strictly greater than 1.5sg.pc 1.5:2.0— this filters structural groups with partial charges between 1.5 and 2.0
These queries can be used in SAMSON’s selection editors or scripts to automate selections, show/hide certain groups, or apply specific materials and labels.
Combining with other attributes
NSL lets you combine multiple criteria for even more refined selections. Suppose you want to find structural groups with large partial charge and more than 10 atoms. You could use:
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sg.pc > 1.5 and sg.nat > 10 |
This query keeps your workspace focused on chemically significant portions of your model, especially useful when analyzing binding sites or charged regions in large proteins or supramolecular systems.
When things get visual
Once filtered, selected groups can be color-coded or rendered differently to highlight regions of interest. If you use this wisely, you can reduce visual clutter and direct attention to key molecular features. This is especially helpful when preparing figures for reports or publications.
Finally, since the partial charge attribute supports floating point filtering, you have granular control. Instead of just worrying about integer charges (as with formalCharge), you can break things down by realistic values derived from quantum calculations or parameterized force fields.
To learn more about selecting structural groups based on partial charge and other attributes such as the number of atoms or chemical elements, visit the documentation page: SAMSON Structural Group Attributes.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.