For molecular modelers using SAMSON, the ability to control visibility and selection at the side chain level can be a game-changer when analyzing complex molecular structures. Let’s explore how the attributes visible and selected can help refine your modeling workflows with unmatched precision.
Why side chain visibility and selection matter
Molecular models often involve intricate structures with numerous side chains that may need to be highlighted, hidden, or selected independently of the main chain. This is particularly useful for fine-tuning visualizations, performing targeted analyses, or preparing presentations.
Working with the visible attribute
The visible attribute, inherited from the node attribute space, allows you to control whether a side chain is rendered in your workspace or hidden from view. This is particularly useful when one needs to declutter the model while focusing on specific areas.
The attribute can take the following values:
true: The side chain is visible.false: The side chain is hidden.
For example, the expression sc.v will return all visible side chains, while not sc.v will return the hidden ones, making it easy to toggle visibility based on your needs.
Refining selections with the selected attribute
The selected attribute, also inherited from the node attribute space, enables you to determine whether a side chain is part of the current selection. Unlike other attributes, this attribute does not have a short name.
The possible values for selected are:
true: The side chain is selected.false: The side chain is not selected.
To apply this attribute, you can use expressions such as sc.selected to return all selected side chains or not sc.selected to exclude them from your selection. This is instrumental in isolating specific side chain features for further analysis or manipulation.
An example of combined use
By combining visible and selected attributes, you can streamline workflows. For instance, if you wish to analyze only the visible and selected side chains, you can use:
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sc.v and sc.selected |
This will help you narrow down your focus without unnecessary distractions caused by hidden or deselected elements.
Learn more
For a deeper dive into these attributes and others, visit the official documentation at SAMSON’s side chain attributes page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at SAMSON Connect.