Understanding and organizing molecular data can sometimes feel overwhelming, especially when working with visually complex models. In SAMSON, the Presentation Attributes provide an efficient way to enhance clarity while controlling how specific elements are displayed. Let’s explore what these attributes can do and how they can streamline your molecular modeling tasks.
What are Presentation Attributes?
Presentation attributes in SAMSON are parameters within the presentation attribute space (or pr for short) that apply exclusively to presentation nodes. These attributes help in customizing how molecular elements are visualized, making it easier to distinguish certain parts, hide unnecessary elements, or emphasize key features.
As a molecular modeler, this can be especially useful when presenting your work or focusing on specific aspects of your model.
Key Presentation Attributes Explained
Here’s an overview of the main presentation attributes you can leverage:
- hidden (pr.h): Use this attribute to hide elements when
true. For instance,pr.hwill hide a corresponding element, whilenot pr.hensures it is visible. - name (pr.n): Assign and filter elements by their names using quoted strings. You can specify exact names (
pr.n "A") or use wildcards (pr.n "L*") to select multiple items at once. - selected: This indicates whether a node is selected. Using
pr.selectedreturns selected elements, whilenot pr.selectedexcludes them. - selectionFlag (pr.sf): A boolean attribute used to handle selection states for nodes. For example, applying
pr.sf falsedisables selection flags. - visibilityFlag (pr.vf): Toggles visibility flags for elements. Use
pr.vf falseto disable visibility flags. - visible (pr.v): Determines if an element is visible. You can easily include or exclude components by toggling
pr.vornot pr.v.
Why Use Presentation Attributes?
Let’s address the common pain of navigating large and intricate molecular models. Searching through hundreds or thousands of nodes can be cumbersome and make analysis nearly impossible. Presentation attributes let you quickly filter and customize node visibility and states without altering the core molecular data.
For example, if you’re preparing a presentation for peers or writing a paper, you might want to hide irrelevant parts of the model or highlight specific components. Attributes like pr.h and pr.n allow you to tailor visualizations with precision, helping you focus or communicate effectively.
Where to Learn More
The best way to familiarize yourself with presentation attributes is by exploring their use in SAMSON. For detailed descriptions and examples of each attribute, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.