Quickly Isolate Molecules in Complex Models with Visibility Filters

If you work with complex molecular systems, you’ve likely faced the challenge of cleaning up crowded views. Structures with hundreds or thousands of molecules can overwhelm your workspace and slow down your workflow. Whether you’re analyzing a protein-ligand interaction or visualizing a synthetic system, sometimes all you need is to isolate specific elements based on their visibility or selection status—without endlessly clicking through the hierarchy.

This is where SAMSON’s Node Specification Language (NSL) offers a clean solution using logical visibility and selection-based filters for molecule nodes. Let’s explore how you can use these features to your advantage.

Filtering Molecules by Visibility Status

Within SAMSON’s NSL, molecule nodes inherit a set of visibility-related Boolean attributes from the generic node attribute space. These include:

• visible (mol.v): Whether the molecule is currently visible in the viewport.
• hidden (mol.h): Whether the molecule has been manually hidden.
• visibilityFlag (mol.vf): A flag controlling rendering visibility.

For example, if you want to select only molecules that are currently visible, you can use:

If you want to exclude hidden molecules:

Need to find invisible molecules for debugging display issues? Try:

Working with Selection Flags

You can also filter based on whether a molecule has been selected:

• selected: True if the molecule is selected. Example:

• selectionFlag (mol.sf): A more technical flag indicating selection status or behavior in logical expressions.

These attributes allow you to automate selection, export, or analysis operations on large systems.

Time-Savers in Practice

Let’s say you’re analyzing a molecular dynamics result and exported multiple conformers. You want to only apply a material color (or remove it) to visible molecules. Using NSL, you can write conditions such as:

This means: modify only molecules that are visible AND don’t already have a material assigned to them.

Or maybe you want to hide all unselected molecules for clarity. Easy:

Select those, and then hide them.

By chaining such expressions, NSL turns the molecular scene into a manageable dataset for fast operations.

Documentation at a Glance

Here’s a table summarizing the most commonly used visibility-related attributes:

Attribute	Short name	Values	Use case
visible	v	true / false	Filter molecules currently visible in the view
hidden	h	true / false	Identify manually hidden molecules
selectionFlag	sf	true / false	Filter based on programmatic selection flags
selected	(none)	true / false	Check if molecule is currently selected

Combining these logical queries allows you to take full control of your molecular setups with minimal friction, making large scene management far easier than relying only on visual intuition or manual editing.

Learn more from the official documentation here.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.