Maestro

Show / Hide Atoms

Click the eye to show or hide all the selected atoms. (When the eye is closed, it will hide your atoms.) If part of the selection is already hidden, the first click will show the atoms; click again to hide them.

Show Only

Click here if you want to show only the selected atoms. All other atoms will be undisplayed.

Show Only Polar Hydrogens

Use this button if you want to hide nonpolar hydrogens - or show polar hydrogens - associated with the selected atoms.

Hydrogens Menu

Click the arrow button next to the Hydrogens button to open a menu with options to hide or show all hydrogens.

Representation

Click to choose the appearance of your selected atoms and bonds.

Color scheme

Click the big button to apply the color scheme shown on the label, or click the arrow button to select a different scheme from the menu.

Single Color

Click the paint bucket to pick a solid color for your selected atoms.

Add / Update Labels

Click this menu button to choose the information you want to see. The "Residue Information" option displays the residue name and number beside the CA atom for each selected residue. The other options apply to all selected atoms.

Delete Labels

Click here to delete the labels from the selected atoms.

Note: Labels will only appear where they are useful and relevant. For instance, "Chirality" will only annotate chiral atoms, and "Formal Charge" will only display for atoms with a non-zero charge.

Add / Update Ribbons

Click the big button to add basic ribbons to all your selected residues. Any existing ribbons within the selection will be updated.

Delete Ribbons

Click here to delete the ribbons from the selected residues.

Tip: To change the appearance of existing ribbons or adjust the visibility of their atoms, select the atoms and right-click on a ribbon segment in the Workspace. Then make the changes in the ribbon editor palette.

Tip: The default ribbon color and style can be changed in the Preferences panel. Bring up the panel and search for "ribbons" to find the page.

Add Molecular Surface

Click to add a basic molecular surface to the selected atoms.

Tip: To hide or delete a surface, or change its appearance, right-click on the surface in the Workspace, avoiding any underlying atoms. (Watch for the mouse pointer to change to a plain arrow.) Then choose the desired action from the special popup menu.

Tip: If a surface is hidden, you can show it again by clicking the blue S at the right of the Title column in the Entry List or Project Table, then choosing the surface name in the menu.

Presets button

Click the main button to apply the Custom Preset to your structure.  This is the fastest way to visualize your binding sites - or apply your own favorite styles with one click.

Presets menu

Click the arrow button if you want to apply a different preset - taken from PyMOL - or edit the Custom one. You can also turn on the "Reapply preset" setting, which automatically applies the Custom Preset to all structures in the Workspace when new entries are included.

Note: Presets apply to all atoms in the Workspace, regardless of visibility or selection.

Tip: The keyboard shortcut for applying the Custom Preset is Control-Y (Command-Y on Mac).  

Tip: To turn on the "Reapply" option without opening the menu, double-click the Presets button.

Edit Custom Preset

You can change the behavior of the Custom Preset by choosing Edit Custom… from the menu and making changes here.

Note: The Preset will be applied when you click OK or Apply.  

Tip: Uncheck the checkbox if you do not want the preset to take a certain action. Check the box and choose "None" or "All" if you want a specific result (e.g., ribbons or labels removed, all ions displayed).

After applying preset

After applying the default Custom Preset