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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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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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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.