How to Instantly Find Hidden Molecular Representations in SAMSON

When working on large or complex molecular models in SAMSON, it’s common to lose track of some representations — especially those that are invisible, hidden, or filtered out due to selection flags. This can quickly become frustrating: Is that surface still loaded? Why can’t I find that representation I created 10 minutes ago?

The good news is that SAMSON’s Node Specification Language (NSL) gives you tools to track — and recover — those elusive presentation nodes without unnecessary clicks. In this blog post, we’ll focus on presentation attributes that control visibility, and show how you can craft simple queries to instantly identify hidden or filtered representations in your document.

Understanding Presentation Nodes

Presentation nodes in SAMSON contain visual representations of other elements, such as surfaces or molecular renderings. When using NSL filters with the pr attribute space, you can search specifically for these presentation nodes and examine their status.

The Usual Pain: Missing Elements

Let’s say you just calculated a molecular surface, but it’s not visible anymore. Could it have been hidden? Or toggled off through a selection flag? The Node Specification Language provides specific filters to answer just that.

Useful Attributes for Finding Hidden Representations

Here are some key presentation attributes and how to use them:

pr.h: Indicates whether a node is hidden. Use pr.h to find all hidden ones.
pr.v: Corresponds to “visible” — a user-friendly way to identify nodes that are (or aren’t) visible in your viewport.
pr.vf: “visibilityFlag” — this internal flag contributes to the node’s visibility status.
pr.sf: “selectionFlag” — when disabled, even selected items may not be processed.

The difference between pr.h and pr.v can be subtle but powerful: pr.h tells you whether the node has been manually hidden from the document tree, while pr.v also reflects other visibility influences (like parent node visibility).

Examples You Can Use Right Now

Looking to find all hidden representations in your document? Use:

pr.h

pr.h

How about everything that’s not currently visible?

not pr.v

not pr.v

Or show every visible surface that starts with the name “L”:

pr.v and pr.n "L*"

1	pr.v and pr.n "L*"

All nodes with selection disabled?

pr.sf false

1	pr.sf false

This kind of filtering becomes especially useful when handling models from collaborators or when returning to older projects.

Combining Filters for Effective Searches

Need to find presentation elements that are in your file but not contributing to the scene?

pr.h or not pr.v

1	pr.h or not pr.v

You can even narrow it down:

(pr.h or not pr.v) and pr.n "Surface*"

1	(pr.h or not pr.v) and pr.n "Surface*"

And It’s Fast

One of the most valuable aspects of working with NSL is speed. These queries work instantly, even in large models.

Understanding and using the presentation attributes in NSL means saving time, reducing frustration, and having full control over what’s shown in your molecular scene.

You can learn more in the documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.