Molecular modelers work with complex systems that often require precise visualization and control over numerous attributes. If you’ve ever struggled with managing the visual representation of your molecular designs, SAMSON’s presentation attributes, defined in the presentation attribute space (or pr for short), provide a highly organized structure for handling these details.
Presentation attributes allow control over how presentation nodes are displayed and interacted with – such as visibility, selection, and naming. Let’s explore some of these key attributes and how they may simplify your workflow in molecular modeling.
The Basics of Presentation Attributes
In SAMSON, presentation attributes, such as hidden, visible, name, and more, help you with the following:
- Creating tailored visualizations for specific components of your molecular structures.
- Easily toggling between states (e.g., visible/invisible, selected/unselected).
- Applying custom names and filters for an organized node structure.
Practical Application of Key Attributes
Here are the most common presentation attributes and tips for their use:
hidden (pr.h)
Use hidden to define whether a node is completely hidden. It takes values true or false, and you can apply it directly like this:
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pr.h true not pr.h |
When working with large molecular models, hiding specific parts of your system can declutter your workspace, helping you focus on the areas of interest.
visible (pr.v)
Unlike hidden, the visible attribute defines whether the node’s visibility is enabled (though not necessarily displayed in all contexts). Use it like:
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pr.v not pr.v |
If you’re scripting or automating processes, toggling visible allows greater control in rendering output scenes or layers.
name (pr.n)
Want to label a specific representation? The name attribute lets you define string labels. It’s particularly useful when working with multiple components. For example:
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pr.n "Backbone" pr.n "L*" |
Using specific naming conventions helps create hierarchical structures for easier navigation and referencing.
selectionFlag (pr.sf) and selected
The selectionFlag and selected attributes manage selection states. Use them to dynamically highlight elements during simulations or data gathering:
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pr.sf false pr.selected |
This is invaluable when pairing visual selection with functional operations, such as applying physical constraints or running calculations on selected nodes.
Streamlining Molecular Design in SAMSON
These presentation attributes may seem small, but they provide significant control over complex visualization workflows. For instance, toggling visibility or assigning meaningful names to different representations adds flexibility and organization to your molecular design approach. Tools like these are designed to reduce visual clutter, eliminate inefficiencies, and help modelers achieve clear, actionable insights into their systems.
For thorough documentation about all presentation attributes, examples of additional properties, and inheritance details, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.