For molecular modelers, clarity in visualization is not a luxury—it’s a necessity. Whether you are analyzing intricate molecular systems or preparing to share your findings, the ability to control what’s visible, what’s emphasized, and what’s hidden can save time and make your work more effective. SAMSON’s presentation attribute space is designed to address this challenge by giving users fine-grained control over how models are displayed. In this post, we’ll explore some key presentation attributes and how they can be used effectively to improve your molecular modeling workflows.
What Are Presentation Attributes?
The presentation attribute space in SAMSON is part of the Node Specification Language (NSL). It helps you define and customize visualization properties of molecular nodes, enabling better control over what’s presented in your models. These attributes are particularly useful for working with presentation nodes, such as those involving rendering or visualization settings. Let’s break down some of the key attributes and explore their applications.
Key Attributes at a Glance
Below is a table summarizing some important presentation attributes and their utility:
| Attribute Name | Short Name | Possible Values | Example Usage |
|---|---|---|---|
| hidden | h |
true, false |
pr.h, not pr.h |
| name | n |
strings in quotes | pr.n "A", pr.n "L*" |
| selected | – | true, false |
pr.selected, not pr.selected |
| selectionFlag | sf |
true, false |
pr.sf, pr.sf false |
| visibilityFlag | vf |
true, false |
pr.vf, pr.vf false |
| visible | v |
true, false |
pr.v, not pr.v |
Examples of Practical Use
Let’s look at how these attributes can help solve common visualization challenges in molecular modeling:
- Hiding Irrelevant Features: Use the
hiddenattribute (pr.h) to exclude parts of your model that aren’t currently needed, making complex systems easier to analyze without distraction. - Highlighting Key Elements: By manipulating the
selectedattribute (pr.selected), you can instantly emphasize specific nodes for presentations or collaborative discussions. - Custom Node Identification: The
nameattribute (pr.n) allows you to search for or filter nodes by their predefined names—especially useful when working with large simulations or assemblies.
These attributes can also be combined with logical expressions to apply advanced filtering logic. For instance, filtering nodes that are both visible (pr.v) and named (e.g., pr.n "Ligand") can streamline many workflows in large-scale projects.
For a deeper dive into all the available attributes, consult the official documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.