When working on complex molecular systems, the ability to quickly select relevant atoms, residues, or molecules is vital. Whether you’re visualizing a protein-ligand interaction, preparing a simulation, or analyzing channels through a membrane, making precise selections can save time and improve accuracy.
In SAMSON, the integrative platform for molecular design, Selection Filters offer a simple yet powerful way to control what gets selected in your workspace. This post dives into how selection filters can help you focus your analysis more effectively without complex configuration.
Why Selection Filters Matter
Let’s say you’re analyzing a protein structure and you just want to select the residues involved in a binding pocket. Using a default selection method might include atoms, side chains, or even unrelated molecules. This quickly becomes cluttered—especially for large biomolecular systems.
This is where Selection Filters help. They act as a lens, allowing you to define what level of the molecular hierarchy your selections operate on. For example, do you want to select atoms, residues, chains, or entire molecules? With a quick switch, you can control this behavior.
Where to Find Selection Filters
Selection filters are accessible in the top-right corner of the viewport in SAMSON. By default, the filter is set to “Any node”, meaning selections can include atoms, residues, molecules, or any other node type available in the document.
Here’s what a few common options do:
- Atoms: Selecting selects only atoms, even if you click on a residue or chain.
- Residues: A click on any atom in a residue selects the whole residue.
- Any node: The default option that allows selections across all levels.
This becomes particularly helpful when using the selection editor or selection commands. For example, a rectangle selection will behave differently based on the active filter: selecting atoms, residues, or molecules entirely changes what gets picked up.
Combining with Select All and Deselect All
The selection filter directly interacts with the Select All (
) and Deselect All (
) commands available next to the filter.
For instance, if the filter is set to “Residues”, clicking Select All will only select residues in the document. The logic is intuitive and lets you perform bulk selections that actually match the granularity of your analysis.
Creating Your Own Filters
Advanced users can define custom filters using the Node Specification Language (NSL). For example, to select only “LYS” or “HIS” residues, the NSL expression would be:
|
1 |
r.t LYS or r.t HIS |
You can save this filter through the Select > Find window, name it, and it will appear in your available list of filters. This allows you to define molecular queries that align with your experimental goals.
Tips for a Cleaner Workflow
- Resetting the filter to “Any node” is a good way to return to general selection behavior.
- Right-click on custom filters to remove them from the list when no longer needed.
- Use selection filters in combination with the Rectangular Selection Editor for precise graphical interactions.
Selection filters are a subtle tool that makes a big difference in clarity and productivity for molecular modeling workflows.
To explore all selection methods in SAMSON, visit the full selection documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.