Maestro User Manual

Chapter 5: Building and Adjusting Structures

Maestro 10.2 User Manual

91

Undo 

Undo the last action. Can be performed multiple times.

Redo 

Redo the last action that was undone. Can be performed multiple times.

Lasso 

Select atoms by drawing around them (“lassoing”). The selected atoms can be moved, rotated, 

deleted, copied.

Move 

Move (translate) the selected atoms or the entire structure. Drag in the drawing area to move 

the structure. Drag the selection to move the selected atoms. (This is the default action for 

dragging a selection, so you do not need to click this button before dragging it.) You can also 

move the structure by dragging with the right mouse button.

Rotate 

Rotate the selected atoms or the entire structure. Drag in the drawing area to rotate the struc-

ture. The angle through which the structure has been rotated is displayed near the center of 

rotation while you are rotating it. If rotation does not seem to be working properly, check 

whether you have other structures in the drawing area that are not visible. You can also rotate 

the structure by dragging with the middle mouse button.

Cleanup 

Clean up the structure (2D coordinates) and normalize orientation and arrangement of groups. 

If you have atoms selected, only those atoms are cleaned up.

Draw 

Draw a single bond. Click on an atom to draw a bond to a new (carbon) atom, click on a bond 

to add another bond between two atoms.

Erase 

Delete atoms or bonds. Clicking on a carbon atom deletes it; clicking on a non-carbon atom 

changes it back to carbon, then clicking again deletes it. Clicking on a bond removes one 

bond.

Wedge Bond 

Draw a wedge bond. Clicking on an atom draws a wedge bond to a new (carbon) atom; click-

ing on a single bond converts it to a wedge bond.

Dashed Bond 

Draw a dashed bond. Clicking on an atom draws a dashed bond to a new (carbon) atom; click-

ing on a single bond converts it to a dashed bond.

Increase Charge 

Increase the formal charge on an atom by 1.

Decrease Charge 

Decrease the formal charge on an atom by 1.

---

Chapter 5: Building and Adjusting Structures

Schrödinger Software Release 2015-2 

92

5.5.3

Sketching Molecules

To start drawing, click the 

Draw

 button. 

Drawing creates a carbon-atom framework. You can change the element with the element

buttons, either during drawing or after you have finished drawing, or by typing the element

symbol while the pointer is over an atom.

The first atom is placed by clicking in the drawing area. It is shown as CH

4

. After placing the

first atom, you can draw in several ways:

• Click on an atom to place a new atom and draw a bond to it from the clicked atom. The

bond is placed in a default orientation with respect to existing bonds.

• Drag from an atom in a particular direction, to place a new atom and draw a bond from

the clicked atom to the new atom in the chosen direction.

• Drag from an atom to another atom to create a bond between the two atoms.

• Hold down shift and drag from an atom to add a linear chain to that atom.

• Click on a bond to increase its bond order.

The “active” atom—the one to which a new bond will be attached—is indicated by a gray

filled circle. Likewise, the active bond is indicated by a thicker gray line. The active atom or

bond changes as you move the pointer over the atoms or bonds.

You can also start your drawing with a ring: click on the ring in the toolbar then click in the

drawing area to place the ring.

To draw bonds with a given stereochemistry, click the 

Wedge Bond

 or 

Dashed Bond

 button,

and draw in the drawing area. Clicking on a bond changes its stereochemistry; clicking on an

atom adds a new atom with the selected orientation.

To add rings to your system, click on one of the ring buttons, then click in the drawing area.

When you move the pointer into the drawing area, the ring is shown in blue. As you move the

pointer in the drawing area, the ring “snaps” to positions that show a potential attachment of

the ring to the structure. Clicking when the ring is in one of these positions places the ring at

that position, and its color changes to black. You can do the same with the fragments on the

User-defined fragments

 toolbar. 

---

Chapter 5: Building and Adjusting Structures

Maestro 10.2 User Manual

93

To add a functional group, pause the pointer over the atom you want to add the group to, then

type – followed by its name, and press 

ENTER

, e.g. -et to add an ethyl group. Many common

functional groups are recognized: the list is given in 

Table 5.1

 with the corresponding

SMARTS patterns; the names are case-insensitive. You can also replace an atom with a func-

tional group, by omitting the initial –. 

To change the element, you can do one of the following:

• Pause the pointer over the atom, then type the element symbol.

• Click the button for the desired element on the toolbar, then click an atom in the structure.

• Type the element symbol, then click an atom in the structure.

The last two of these choices allow you to click on multiple atoms to change the element; the

first operates only on the active atom.

To assign a formal charge, click the 

Increase Charge

 button or the 

Decrease Charge

 button,

then click on an atom. The formal charge is given next to the atom, and any hydrogens are also

shown that are needed to complete the valence for the atom; or a red underline is shown to indi-

cate that the valence is not satisfied. You can also pause the pointer over an atom and type in

the formal charge. Any combination of numbers, +, and – is accepted.

Table 5.1. Functional group names and SMARTS patterns for use in editing 2D structures.

Name

SMARTS

Name

SMARTS

Name

SMARTS

me C

ph  C(C=C1)=C-C=C1

coo- 

C(=O)[O-]

et CC

bz CC(C=C1)=C-C=C1

no2 

[N+](=O)[O-]

pr CCC

chex 

C(CC1)CCC1

so2 

S(=O)=O

ipr C(C)C

cp  C(C=C1)C=C1

so2n 

S(=O)(=O)N

nbu CCCC

ome OC

so3  S(=O)(=O)[O-]

ibu CC(C)C

oet OCC

po3 P(=O)([O-])[O-]

sbu C(C)CC

cooh 

C(=O)O

con C(=O)N

tbu C(C)(C)C

coome 

C(=O)OC

nco NC=O

nhex CCCCCC

cooet C(=O)OCC

cn 

C#N

---