Maestro User Manual

Chapter 5: Building and Adjusting Structures

Schrödinger Software Release 2015-2 

94

To move a group, first select the group by drawing around it with the 

Lasso

 tool:

If you want to translate it, just drag it to the new location. The pointer must be over the group

when you start to drag it. If you want to rotate it, click the 

Rotate

 button,

then drag it to the new orientation. As for translation, the pointer must be over the group when

you start to drag it. The angle is displayed as you drag.

To adjust the view, you can zoom in or out with the scroll wheel or pinch gesture, pan (trans-

late) with the right mouse button, and rotate with the middle mouse button.

5.5.4

Saving Templates for Building

You can save structures as templates that you can use to build other structures. These templates

are displayed on the 

User-defined fragments

 toolbar, which you display by choosing 

View

 

→

User defined fragments

. When you have drawn a structure that you want to add to the toolbar,

press 

CTRL

 (



) and drag the structure to the toolbar. A new button is added with the structure

displayed on it. To remove a structure from the toolbar, click on the button and press 

DELETE

or 

BACKSPACE

. You can use these fragments in the same way as the ones on the main toolbar.

5.5.5

Saving Structures

You can save a structure as a project entry in several ways, with the buttons at the bottom of the

panel:

•

Replace Workspace

—Replace the Workspace with the sketched structure, as a scratch

entry. 

•

Create New Entry

—Create a project entry from the structure in the drawing area. A

default title is assigned to the entry. Hydrogens are added to the structure; it is converted

to 3D if 

Convert to 3D

 is selected. 

•

Update Entry

—Update the project entry from which the structure was taken with the

updated structure in the drawing area. Hydrogens are added to the structure; it is con-

verted to 3D if Convert to 3D is selected. 

If you have a LigPrep license, you can convert it to 3D by selecting 

Convert to 3D

; otherwise it

is added as a 2D structure, and you must convert it to 3D if you want to use it for calculations.

Hydrogens are always added when saving a structure as a project entry.

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Chapter 5: Building and Adjusting Structures

Maestro 10.2 User Manual

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To save an image of the structure in PNG, JPEG, or BMP format, press 

CTRL+ALT+P

. A dialog

box opens with controls for the size of the image and an option for saving with a transparent

background. When you click 

OK

, a file selector opens, in which you can navigate to the loca-

tion and name the file. The image type is determined by the file extension. 

5.6

Changing Elements

Whether you build a molecule in Place mode, Grow mode, or Draw mode, the range of

elements available to you by default is limited. Even with access to the whole range of

elements, it is often more efficient to quickly sketch a structure as a carbon skeleton and then

change the elements to the desired ones afterwards. You do not have to complete the structure

before you make the change, you only have to place an atom at the desired location. 

Changing an atom from one element to another can be done from the 

Build

 toolbar, the 

Selec-

tion

 shortcut menu, or from the 

Atom Properties

 tab. 

Figure 5.5. The Atom Properties tab showing tools for the Element property.

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Chapter 5: Building and Adjusting Structures

Schrödinger Software Release 2015-2 

96

From the 

Set Element

 button menu on the 

Build

 toolbar you can choose H, C, N, O, P, S, F, Cl,

Br, I, Al, or Si, then click on an atom in the Workspace to change it to the selected element. 

To change to other elements, you can choose 

Other

 on the button menu and select an element

in the element selector (see 

Figure 5.3 on page 87

). The element is listed in parentheses after

Other

 on the button menu, to indicate that it is the current element. 

T

o use the shortcut menu, select the atoms to change, then right-click in the Workspace and

choose 

Set Element

, then choose the element. The same range of elements is available as on

the toolbar button, and also the 

Other

 item for choosing other elements.

To use the 

Atom Properties

 tab in the 

Build

 panel, first choose 

Element

 from the 

Property

option menu. A periodic table is displayed, from which you can select an element, then click

on an atom in the Workspace to change it to that element. You do not need to select 

Set

Element

: this is done automatically when you click on an element in the periodic table.

However, you can select 

Set Element

 if it is unselected and you want to use the currently

selected element. 

5.7

Changing the Bond Order and Formal Charge

After creating a structure, you may wish to change some of the bond orders or formal charges.

You can make these changes with the tools on the 

Build

 toolbar (as shown below) or by right-

clicking a bond and choosing the appropriate item from the shortcut menu.

• To increase the bond order, click the 

+ Bond Order

 toolbar button

then click the bonds whose order you want to increase. Each click increments the bond

order by one, up to a maximum of three. You can also increase the bond order in Draw

mode by drawing another bond between the two atoms. 

• To decrease the bond order, click the 

- Bond Order

 toolbar button

then click the bonds whose order you want to decrease. Each click decrements the bond

order by one, to a minimum of 0. Zero-order bonds are displayed with dashed lines in

wire representation and tube segments in tube representation.

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