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.
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.
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).