Molecular modelers often work with large biomolecular systems, such as proteins, and need a quick way to detect modeling issues that could affect visualization, analysis, or simulation. One commonly overlooked issue is the presence of side chains lacking material definitions—the properties that determine how a structure appears or behaves visually. This can make these parts of the structure invisible or misleading in the graphical interface, especially when rendering molecular scenes for publication or presentations.
Fortunately, the Node Specification Language (NSL) within SAMSON offers a convenient way to query and fix such issues. In this post, we focus on the hasMaterial attribute for side chain nodes and how it can be used to track down missing materials in your molecular model.
Why materials matter in side chains
In SAMSON, materials define visual properties—such as color, opacity, and shaders—of molecular elements. When a side chain lacks a material, it may not show up clearly or at all in the viewport. This can lead to confusion during visual inspections, especially when preparing structures for sharing or export.
The hasMaterial attribute helps answer a simple but important question: “Does this side chain have an associated visual material?”
Filtering side chains: Practical NSL tips
With the NSL, you can write concise queries to find problematic parts of your model. For side chains, the short reference is sc, so sc.hm checks if a side chain has a material, and not sc.hm finds those that don’t.
Here’s how you can use it practically:
- To highlight all side chains with missing materials:
not sc.hm - To isolate and show side chains with properly defined materials:
sc.hm - Combine with visibility to detect invisible but defined side chains:
sc.hm and not sc.v
What to do once you’ve identified them
If you discover side chains without materials, double-clicking them in the viewport or the document view should highlight their location. You can then manually assign materials or use default presets to correct their visualization. This is especially useful before running simulations or capturing images.
Useful combinations
The usefulness of sc.hm increases when combined with other attributes, such as sc.name for identifying specific residues, or sc.selected to act only on currently selected elements. For instance:
sc.name "L*" and not sc.hmto find all side chains starting with L that lack a material.sc.selected and not sc.hmto update only selected side chains missing materials.
Conclusion
Proper material assignment is an important aspect of molecular modeling, especially when visual presentation matters. By using sc.hm in the Node Specification Language, SAMSON users can quickly identify and correct missing materials from side chains, ensuring cleaner visuals and fewer surprises during analysis and simulations.
To learn more, visit the full documentation page on side chain attributes in NSL.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.