When working on complex molecular structures in SAMSON, how you see your models can make a real difference. Whether you are analyzing a protein-ligand interaction, presenting your findings, or debugging a simulation, using the appropriate visual model can simplify interpretation and improve communication. Yet many users overlook this and stick with default settings.
In SAMSON’s Node Specification Language (NSL), you can precisely query and manipulate nodes based on their visual representations. The attribute node.category (short name: n.c) includes a set of visual model categories that let you select types of molecular representations like ball-and-stick, ribbon, surfaces, and more. Here’s how to make the most of this forgotten feature.
Why visual models matter
Different representations highlight different aspects of molecular systems:
- Ball-and-stick (short name:
bas): clear atom and bond topology. - Van der Waals (
vdw): shows the actual volume occupied. - Cartoon or Ribbon (
car,rib): ideal for viewing protein secondary structures. - Gaussian surfaces (
gau) or solvent surfaces (sas,ses): useful for molecular accessibility visualization.
Selecting or filtering based on visual models is helpful when customizing renderings, scripts, or performing batch operations. Let’s look at how this is done with NSL.
Using NSL to select visual model types
Here are some common examples:
node.category ballAndStick→ selects all ball-and-stick models.n.c lic, rib→ selects both licorice and ribbon representations.n.c vdw in n.t vm→ filters van der Waals visual models among visual model nodes.not n.c ses→ exclude solvent excluded surfaces from a selection.
These expressions are concise but powerful, especially when used in scripts or search bars inside SAMSON.
Practical use cases
- Exporting publication images: Need only ribbon and surface models in your scene export? Use
n.c rib, surto isolate them quickly. - Clear UI while modeling: Hide all cartoon models during atom placement:
not n.c car. - Batched updates: Change color scheme based on visual model category. For example, all
basmodels get one color, allvdwanother.
List of supported visual model categories
| Model | Short Name |
|---|---|
| ballAndStick | bas |
| licorice | lic |
| vanDerWaals | vdw |
| cartoon | car |
| ribbon | rib |
| tube | tub |
| gaussianSurface | gau |
| solventAccessibleSurface | sas |
| solventExcludedSurface | ses |
| surface | sur |
NSL makes it easy to manage these views programmatically, and the short names reduce unnecessary typing.
Conclusion
Visual model filtering may sound like a small thing, but in large models with mixed renderings and node types, it can save time, avoid mistakes, and streamline your workflow. Use NSL’s visual model categories to filter, style, or isolate elements more efficiently—and perhaps finally answer “why doesn’t this show up in my render?” 😊
To learn more about visual model categories and other NSL expressions, visit the official documentation page at https://documentation.samson-connect.net/users/latest/nsl/node/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.