Cool Tips and Tricks for Working with Maestro

Advanced Selection Techniques

The Selection Toolbar makes it easy to choose common objects and create complex selections, but some of the most powerful techniques may be more difficult to find. These advanced approaches and tools are described below.

Tips for Working with Selections

Selecting more in the Workspace

You can switch between picking atoms and picking residues without changing your pick level. Just double-click the atom to expand the selection to the residue or small molecule. You can even triple-click to expand it out to the whole molecule or protein.

Double-clicking works at higher levels, too. If you double-click an atom with your pick level set to Residues, you will select the whole molecule or protein.

Clearing the selection from a group of atoms

You might know that holding down Shift while dragging your mouse across a set of atoms adds those atoms to your selection - but how do you unselect them? Click the Subtractive (-) picking button on the Selection Toolbar before dragging out your rectangle in the Workspace. All the atoms in the rectangle will be removed from the selection, and if you are at a higher pick level, the selection will be cleared out to the corresponding level.

Note: This technique works with the Trackpad mouse actions, but you must still press the Shift key while dragging.

Adding or subtracting common objects

You can add a common object to your current selection by turning on Additive (+) picking before choosing the object from the Quick Select section of the toolbar. The ADD button will appear as a reminder that you are adding.

Similarly, you can remove an object from your selection by turning on Subtractive (-) picking. For instance, to select only the hydrogens from your waters, select Waters and then remove Heavy Atoms. The REMOVE button is a reminder that you are removing atoms from the selection.

Click ADD or REMOVE to exit the special picking mode.

Defining specific selections

You can create very specific selections using the Atom Selection Dialog, available from the Define… button on the Selection Toolbar. This dialog lets you query for atoms using combinations of attributes such as Residue Name or Classification, Formal Charge or Element. However, many of the most common selection scenarios can be handled using the toolbar itself, especially when combined with the Structure Hierarchy.

Growing by distance

You can widen your current selection by a particular distance (in Å) by clicking the Expand button and choosing a radius. If you want to select only the atoms in that radius - clearing the current selection - check the Unselect Selected Atoms option before choosing the radius.

Growing by matching

If you want to select all the atoms or residues of a particular type or style, use the Add Matching Items option in the Expand button menu. Start by selecting one or more examples of the things you want to select, then pick the menu item for the matching property. For example, if you want to select all the residues styled in “tube” or “thin tube”, select one of each kind and click Expand > Add Matching Items > Same Representation.

Selecting with ribbons

You can select atoms using the residue ribbons, even when the atoms themselves aren’t visible. Clicking a piece of ribbon is like clicking the CA atom for that residue, so depending on your pick level, you can select just the CA, the entire residue, or the entire protein. Additive (+) and Subtractive (-) picking work as well.

Selection highlighting is also provided. If you put your mouse over a ribbon segment, both the segment and its associated atoms are highlighted. If the atoms are hidden, a temporary representation will appear. This is especially useful at the residue pick level: just move your mouse to review the hidden side chains.

Saving selections

Save your current selection by pressing Ctrl+1 or Ctrl+2... up to Ctrl+0 (Mac users press Cmd+1, etc.). To restore this selection, press the corresponding single digit on the keyboard (1 or 2…). The atoms from your earlier selection will be selected.

Note: Saved selections are only preserved for the current Maestro session. To create a permanent selection that is stored with the project, use Custom Sets. These can be saved from the Atom Selection Dialog and may include abstract objects such as ligands and residue types.

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