Drawing Structures

Maestro has two ways of drawing structures: in 2D and in 3D.

To draw structures in 2D, as you would on paper, you can use the 2D Sketcher Panel. The structure you draw can then be saved as a project entry, either in 2D or converted to 3D. Full details are given in the 2D Sketcher Panel topic.

To draw structures in 3D, you can use the Draw tool in the 3D Builder panel, which you open by clicking the Build toolbar button.

Click the Draw button in the 3D Builder panel to enter drawing mode.

The Draw Structure banner is displayed, with tools for drawing the structure.

There are three action modes, which you select with the two buttons on the left of the palette. These modes are described below. You can change the view (rotate, translate) with the usual mouse actions.

• Draw mode. Click the pencil icon to start drawing.
  
  The pencil icon is highlighted and the cursor changes to a pencil.

  Dragging draws a bond between two atoms. If you press or release on empty space, an atom is added at that point so that there is an atom to draw the bond to or from. Otherwise the bond is drawn from the atom you press on to the atom you release on. Drawing a bond to a new atom places the atom with the same z coordinate as the atom that you drew from. When a new atom is added on pressing, it is placed with z = 0. To place atoms in different orientations, you can rotate the view before placing.

  Note: In the BioLuminate or Materials Science profiles, you must hold down the Shift key while dragging, as dragging with the left mouse button performs rotations. The same is true if you switch to PyMol or Trackpad mouse mode in the Maestro profile (see Customize Mouse Actions Panel).

  Clicking on a bond increases the bond order. You can also drag between two atoms with an existing bond to increase the bond order.

  To add atoms of a different element, click the element on the palette. Drawing bonds now adds atoms of the new element, but does not change the element for existing atoms. However, you can click on an atom (without dragging) to change the element of an existing atom. If the element you want isn't on the palette, click the ... button to open a periodic table and select the element. The element is placed on one of the two buttons above this button, so you have immediate access to it later.

  When you perform a drawing operation, you can automatically add or remove hydrogens to complete the valence. This action is controlled by the Adjust number of hydrogens following build operations preference, under Builder - Behavior in the Preferences Panel. Turning this preference on does not add hydrogens to existing atoms with unsatisfied valence—to do that, switch to select mode, select the atoms, and click the Add hydrogens button in the Build panel, or choose Edit → Add Hydrogens.
  

  Drawing does not necessarily produce good geometries. The last-drawn bond can be automatically minimized if you select Minimize in the banner. The bond distance and angles involving the two atoms in this bond are updated by minimizing the energy with the current force field. If you want to minimize more atoms, you can switch to select mode, select the atoms, and click the Minimize button in the Build panel.
  

• Erase mode. Click the erase icon to erase atoms and bonds.
  
  The banner title changes to Draw Structure - Erase, the icon is highlighted, and the cursor changes to an eraser.

  Click on an atom to erase it. Click on a single bond to delete the bond, but retain the atoms. Clicking on a double or triple bond erases one bond, i.e. decreases the bond order.

• Select mode. Click the current highlighted mode icon to deselect it.

  The banner title changes to Draw Structure - Select, and neither icon is highlighted. You can now select atoms with the usual selection operations, and perform actions on the selection (e.g. with the shortcut menu). Some useful actions for drawing are to minimize the selected atoms, delete them, or add hydrogens.