Maestro User Manual

Chapter 5: Building and Adjusting Structures

Schrödinger Software Release 2015-2 

88

• To begin drawing with the currently selected element, click the 

Draw 

button.

The 

Draw structures 

button appears indented, indicating that you are in Draw mode. The

default element is carbon. 

• To place an atom, click in the Workspace. 

The atom appears as an asterisk enclosed in a purple cube. The cube marks the “active”

atom, which means that it is automatically bonded to the atom that is placed next. Each

subsequent click in the Workspace places another atom and bonds it to the previous atom

with a single bond. To finish drawing, click the active atom. The cube vanishes. 

• To start drawing from another location in the structure, deactivate the active atom by

clicking on it, then click on the atom that you want to start drawing from. This atom

becomes the active atom. 

• To connect the active atom to an existing atom, click the existing atom. 

• To create a multiple bond between the active atom and an adjacent atom, click the adja-

cent atom. Another bond is added between the two atoms. 

• To change the element that you are drawing with, choose the element from the 

Draw

 but-

ton menu, or choose 

Other

 and select it in the element selector. The next new atom you

place will be an atom of the new element. If you connect existing atoms of a different ele-

ment, the element of the existing atom is not changed: thus, it does not matter which ele-

ment is selected when you draw a bond between two existing atoms.

The atoms that you draw are placed in the xy plane (the plane of the screen). If you want to

create a 3D structure, you can rotate the structure in the Workspace with the middle mouse

button, then continue drawing atoms. Rotation does not change the active atom or exit Draw

mode. You can also move atoms that you have placed using the 

Move

 button menu. 

To move an atom in the xy plane, choose 

X-Y

 from the button menu, click the atom you want to

move, then click the new location. If the atom is in a ring, only the atom is moved. If the atom

is not in a ring, the atom and its attached atoms are moved. To move an atom in the z direction,

choose 

+Z

 or 

-Z

 from the menu, and click the atom to be moved. The atom is moved 0.5 Å in

the chosen direction. 

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Chapter 5: Building and Adjusting Structures

Maestro 10.2 User Manual

89

5.5

Building a Structure in 2D

Draw mode (

Section 5.4

) allows you to build a structure in 3D by drawing in the Workspace.

Maestro offers another tool, for sketching structures in 2D. The structures can be saved as

project entries, either with 2D coordinates, or converted to 3D with LigPrep. 2D structures can

be sketched in the 

2D Workspace

 panel, which you open by choosing 

Edit 

→

 2D Sketcher

, or

clicking the 

Sketcher

 button on the 

Edit

 toolbar.

The 

2D Sketcher

 dialog box has a menu bar at the top, a drawing area, a toolbar to the left of

the drawing area, and options for creating a project entry below the drawing area. 

Figure 5.4. The 2D Sketcher panel.

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Chapter 5: Building and Adjusting Structures

Schrödinger Software Release 2015-2 

90

5.5.1

The 2D Sketcher Menu Bar

The menu bar has three menus: 

File

, 

Edit

, and 

View

. The 

File

 menu has a single item, 

Save

Screenshot

, which saves an image of the drawing area in a file. The image can be saved in

PNG, JPG, or BMP format. The shortcut key is 

CTRL+ALT+P (

P)

. 

The 

Edit

 menu has the usual 

Undo

 (

CTRL+Z

, 

Z

) and 

Redo

, 

Copy

 (

CTRL+C

, 

C

) and 

Paste

(

CTRL+V

, 

V

) items. 

Copy

 copies the selected atoms or the entire structure to the clipboard as

a SMILES string. 

Paste

 places the SMILES string in the center of the display area as a 2D

structure. 

Select All

 (

CTRL+A

, 

A

) and 

Deselect

 (

CTRL+D

, 

D

) select all atoms and clear the

selection. 

Cleanup

 cleans up the structure (2D coordinates) and normalizes the orientation and

arrangement of groups.

The two remaining items on the 

Edit

 menu allow you to get structures from other sources:

•

Input SMILES String

  (

CTRL+S

, 

S

) allows you to add a structure to the center of the

drawing area by specifying its SMILES string in a dialog box. 

•

Common or IUPAC Name Search

 (

CTRL+P

, 

P

) allows you to run a PubChem query (on

the web) on the common name or IUPAC name of a structure that you provide in a dialog

box. The first result is added as a 2D structure to the center of the drawing area.

The 

View

 menu has items for flipping the structure, zooming in or out, changing the back-

ground, and labeling or coloring atoms. 

Flip Vertical

 (

CTRL+ALT+F

, 

F

) flips the structure

from top to bottom, and 

Flip Horizontal

 (

CTRL+ALT+H

, 

H

) flips the structure from left to

right. 

Fit to Screen

 (

CTRL+F

, 

F

) zooms in or out so that the structure fills the visible part of

the drawing area. If you prefer to see the structure in white on a black background, like on a

blackboard, choose 

Blackboard View

 (

CTRL+I

, 

I

). Finally, choose User defined fragments to

show or hide the User-defined fragments toolbar.

You can label chiral atoms with R or S by choosing 

Stereochemistry Labels

 (

CTRL+L

, 

L

),

and you can color atoms other than carbon by choosing 

Color Heteroatoms

 (

CTRL+T

, 

T

). N

is blue, O is red, S is yellow, and so on. 

5.5.2

The 2D Sketcher Toolbar

The toolbar has three sets of buttons. The first set of buttons is for performing actions, which

are described below. The second set is a collection of rings that you can add to the structure.

The third set is a collection of elements, which you can use to change atoms to a chosen

element. The selection of the element can also be done by typing the element symbol (case

insensitive). 

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