One of the frequent challenges molecular modelers face is managing complex molecular scenes. When proteins, ligands, and other entities start piling up in your workspace, things can quickly become visually overwhelming. This can make it difficult to focus on specific elements of a molecular system, such as side chains in proteins.
Fortunately, if you’re using the SAMSON platform, there’s a precise and effective way to control what appears on screen: the use of visibility attributes — especially for side chains — through the Node Specification Language (NSL).
Why Control Side Chain Visibility?
Side chains are often the most chemically diverse parts of amino acids. Depending on your analysis — whether it’s docking, mutation scanning, or understanding protein-ligand interaction — you might want to:
- Hide all side chains to focus on the backbone.
- Show only selected or charged side chains.
- Filter visible chains by specific residue names or patterns.
The NSL in SAMSON allows you to do all of this with simple expressions.
The Key Attributes for Side Chain Visibility
In NSL, side chain attributes are accessed using the sc prefix. For visibility-related tasks, you have several relevant attributes:
sc.v: direct visibility of the side chain.sc.vf: visibility flag (might be inherited or controlled by parent structure).sc.h: hidden status.
Each of these attributes is Boolean — you can test for true or false. You can also negate any of them using not.
Examples in Practice
Here are a few practical queries you can use in SAMSON’s NSL to refine side chain visibility:
- Show only visible side chains:
sc.v - Hide all side chains:
First select all side chains:sc
Then toggle their visibility. - Select side chains not currently visible:
not sc.v - Show side chains with visibility flag off:
not sc.vf
This targeted control can dramatically improve your workflow efficiency, especially when working with large or crowded molecular systems.
What’s the Difference between visible and visibilityFlag?
It’s worth noting that visible (sc.v) describes whether the side chain is currently visible in the workspace. On the other hand, visibilityFlag (sc.vf) may reflect inherited visibility settings from a parent node. To fully control side chain appearance, you might need to work with both.
Similarly, using sc.h (hidden) allows for another layer of visibility control — perhaps to force the side chain to stay hidden despite other visibility toggles. Understanding the interaction between these layers helps fine-tune your visualization strategy.
When to Use This
This becomes particularly helpful if you’re:
- Preparing clean visuals for presentations or publications.
- Running simulations where only key residues matter visually.
- Exploring protein interfaces without side chains cluttering the view.
Controlled visibility isn’t just cosmetic. It helps reduce cognitive load and lets you quickly spot what matters most.
To learn more about all available side chain attributes in NSL and how to structure complex queries, visit the full documentation page:
NSL Side Chain Attributes – SAMSON Documentation
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net