Workspace Navigator

Structure Hierarchy

The Structure Hierarchy displays all the entries that are included in the Workspace, allowing you to review each structure in detail, locate individual substructures, and change how they are displayed. Clicking an object in the tree selects the corresponding atoms in the Workspace. Double-clicking it selects it and zooms it into view.

Working with Structures in the Workspace

Browsing the structure

Click on the arrows in the tree to view the contents of the folders.

Each entry included in the Workspace appears as a separate folder under All. Depending on the entry, these folders contain sub-folders for each type of content - Ligands, Protein (or DNA/RNA), Solvents, Other.

The Protein folder holds a set of Chain folders, each of which contains individual residues. Residues and small molecules are the lowest levels of the tree, as shown.


Click the name of an object in the tree to select the corresponding atoms in the Workspace. Use Ctrl-Click (Cmd-Click on Mac) to add objects or remove them from the selection, and Shift-Click to select a range.

Note: A bright blue highlight on a folder means all its children are selected. A duller blue means some children are not selected.

Tip: Selections made in the Workspace are reflected in the tree, but residues and small molecules will show the bright blue selection even if just one atom is selected. You may need to toggle the selection in the tree to ensure that the whole item is selected.


Click into the square at the left to show or hide the corresponding object in the Workspace.

Folder-level objects will appear partially visible (blue triangle) if at least one of their child objects is not displayed. Click the triangle once to display the entire object, twice to hide it.

Tip: Residues and small molecules are considered displayed if at least one of their atoms is visible, so you may have to click the square twice to make these objects fully visible.


You can style individual objects in the tree, regardless of what is selected in the Workspace. Just hover your mouse over the object and click the plus button that appears at the right. The Style Toolbox that opens there will apply to the object on that row of the tree.

Searching the tree

Click the magnifying glass icon to open the Search field. As you type into the field, the tree is filtered to show only matching items (and their parent folders). Double-click on items to locate them in the Workspace. You can also select them or change their display as usual.

To clear the Search, click the small gray X button at the right, then toggle the magnifying glass to hide the field.

Note: Actions on folder-level objects will always affect all children, not just the ones currently displayed in the filtered tree. To select only the matching items within a folder, use Shift-Click (range selection).

Topics covered in this Webinar:

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