For molecular modelers using SAMSON, managing how molecular structures are visually represented can make a significant difference in streamlining workflows and improving clarity during analysis. This challenge is addressed through the presentation attributes of SAMSON’s Node Specification Language (NSL), which allow users to efficiently control the visibility, selection, and organization of their presentation nodes.
What Are Presentation Attributes?
The presentation attributes in NSL apply specifically to presentation nodes. They give users a suite of tools to define how nodes are displayed in their molecular models, providing clarity and control over even large and complex datasets. These attributes include options to manage visibility, selection status, and naming conventions. This blog post explores these attributes and how they can save time and effort for molecular modelers.
Main Presentation Attributes and Use Cases
Below is a summary of the key attributes in the presentation space, their possible values, and how you can use them:
| Attribute Name | Short Name | Possible Values | Examples |
|---|---|---|---|
| hidden | h |
true, false |
pr.hnot pr.h |
| name | n |
strings in quotes | pr.n "Structure A"pr.n "Ligand*" |
| selected | None | true, false |
pr.selectednot pr.selected |
| visibilityFlag | vf |
true, false |
pr.vf falsepr.vf |
| visible | v |
true, false |
pr.vnot pr.v |
A Practical Example
Imagine you are working with a large molecular complex to analyze specific ligands within the structure. You can use the name attribute to identify the ligands by name or pattern:
|
1 |
pr.n "Ligand*" |
This will match all presentation nodes whose names start with “Ligand.” You can then combine this with other attributes like visible or hidden to further refine the visualization setup:
|
1 |
pr.n "Ligand*" and pr.v |
This expression specifies that only ligands matching the name pattern and currently visible will be considered. Such expressions can neatly simplify working with nodes in highly complex molecular models.
Why It Matters
Understanding these attributes allows molecular modelers to move beyond default visualization settings, focusing on conveying only the necessary information. This is especially helpful when presenting structures to a wider scientific audience or collaborating within a team.
Learn More
For a comprehensive overview of NSL’s presentation attributes, check out the official documentation. From visibility management to custom naming, mastering this attribute space empowers you to work more efficiently with molecular structures in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.