Showing and Hiding Atoms

alternate positions, locations

When structures in the Workspace have a lot of atoms, it can be useful to hide some of them, and show only the ones you are interested in. To show or hide atoms, first you must select them. Although hidden atoms can't be selected by picking, they can still be selected as part of an atom group, e.g. protein or ligand.

You can show or hide atoms from the following locations:

  • Style toolbox: The Style Toolbox has buttons for showing or hiding atoms.

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    Show or hide the selected atoms. If all selected atoms are visible, the hide icon (closed eye) is displayed; if there are some hidden atoms in the selection, the show icon (open eye) is displayed.

    Show the selected atoms and hide the unselected atoms. This action is taken regardless of whether the selection includes visible or hidden atoms.

    Show polar hydrogens and hide other hydrogens. Clicking the arrow offers other options for hydrogen atoms: Hide All Hydrogens, Show All Hydrogens.

  • Structure Hierarchy: To show or hide the structure component represented by a row in the Structure Hierarchy, click the visibility button on the left.

    You can also click the button on the right to show the Style Toolbox, where you can use the buttons described above with the structure component as the selected atoms.

    For hydrogen atoms, the settings button has an option, Display Polar H Only, which controls the display of hydrogens when using the Structure Hierarchy to display or hide structures. It does not affect existing structures; it applies only to subsequent display actions. See Structure Hierarchy (Hierarchy) for more information.

  • Shortcut menu: To hide the selected atoms, right-click on a selected atom and choose Undisplay.

  • Workspace Configuration toolbox: You can show or hide some kinds of crystal-related atoms with the following tools from the Workspace Configuration Toolbox:

    Show atoms that are alternate positions for existing atoms, as "ghost" atoms. These alternate positions come from crystal structures where a set of atoms occupy two different positions in the crystal, e.g. two rotamers of a protein side chain. You can switch between the two sets of positions—see Selecting Rotamers and Torsions