Maestro User Manual

Chapter 4: Viewing the Workspace

Maestro 10.2 User Manual

65

4.2.1

Translating the View

Translations can be carried out with the right mouse button, as described in 

Table 4.1

.

You can perform translations in increments along the x, y, and z axes with the keyboard keys

and the corresponding items under 

View

 

→ 

Translate

. The keys are described in 

Table 2.7 on

page 32

.

You can also do a translation by “spot-centering”, an action that places the coordinate origin of

the view on a particular atom, which then appears at the center of the Workspace. As a conse-

quence, subsequent rotations of the view are performed about this atom. This action is done by

right-clicking on the atom. 

In addition to the mouse controls, a number of global transformations are available from the

View

 menu and the main toolbar. 

4.2.2

Rotating the View

In addition to the rotations that can be performed with the middle mouse button, there are a

number of other actions that perform a rotation. 

On the toolbar, there are two buttons for rotation by 90

° about the x axis or the y axis: 

These buttons have corresponding menu items, 

View

 

→ 

Rotate 

→

 X 90

 and 

View

 

→ 

Rotate 

→

Y 90

. 

You can perform rotations in increments about the x, y, and z axes with the keyboard keys and

the corresponding items under 

View

 

→ 

Rotate

. The keys are described in 

Table 2.7 on page 32

.

Another rotation that you can perform is to align the view so that selected atoms are lying on

one of the Cartesian axes or planes. This action is performed in the 

Align Atoms

 panel, which

you open by choosing 

View 

→

 Align

. 

To align two atoms to one of the Cartesian axes, select the axis, select 

Pick atoms

, then pick the

two atoms. A purple cube is drawn around the first atom when you pick it, and the alignment is

performed when you pick the second atom. The view is rotated through the smallest possible

angle to perform the alignment.

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Chapter 4: Viewing the Workspace

Schrödinger Software Release 2015-2 

66

Figure 4.1. The Align Atoms panel.

To align three atoms to one of the Cartesian planes, select the plane, then use the picking tools

in the 

Pick atoms to align

 section to pick the three atoms. When the third atom is picked and a

check is performed to ensure that the plane is uniquely defined (i.e. the atoms are not

collinear), a blue-green plane is displayed in the Workspace, and the 

Align

 button becomes

available. Click this button to perform the alignment. The view is rotated through the minimum

angle required to bring the selected atoms into alignment with the chosen plane. If you do not

want to see the plane, deselect 

Markers

.

When you have done the alignment, you can also change the coordinates of the structure to

those of the current view, by clicking 

Update Coordinates

. The structure itself is then aligned

on the axis or plane, and not just the view of the structure.

4.2.3

Zooming In and Out

Zooming in and out can be done with the scroll wheel, with the middle and right mouse buttons

(held down together), with 

SHIFT+CTRL

 and the middle mouse button, or with the pinch

gesture on a trackpad. The keys 

K

 and 

J

 are assigned to zooming in and zooming out, in small

increments. Each press of one of these keys corresponds to one click of the scroll wheel, and

you can hold the keys down for continuous zoom. 

Another way of zooming is to use the 

Fit to Workspace

 button on the toolbar, which zooms in

or out so that the atom selection fills the Workspace (or all atoms, if there is no selection). 

You can perform a fit to the Workspace from the 

View

 menu. The 

Fit to Workspace

 submenu

offers the choices of 

Selected Atoms

 (shortcut 

Z

), 

All

, or 

Ligand

 (shortcut 

L

). Choosing 

All

allows you to fit the entire structure to the Workspace without changing the selection.

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Chapter 4: Viewing the Workspace

Maestro 10.2 User Manual

67

4.2.4

Restoring the Default View

To restore the view to the default view, in which the view axes are aligned with the coordinate

axes of the structure, click the 

Reset View 

button on the toolbar.

4.2.5

Setting the View Origin and Rotation Center

By default, the origin of the view coordinate system moves when you translate a structure, so

that rotation of the view has the same effect on the structures no matter where they are trans-

lated to. The origin is changed by spot-centering, which was described in 

Section 4.2.1 on

page 65

. The origin is reset when you restore the default view, and it is also set when you do a

Fit to Workspace. 

If you want the center for rotation to stay at the same location regardless of how you translate

the structures, you can set a preference in the 

Preferences

 panel. Choose 

Maestro 

→

 Prefer-

ences

 to open the panel, then in the 

Workspace

 tab, select 

Keep center of rotation fixed while

translating

. The rotation center is then decoupled from the translation origin, and remains at the

location of the view origin when you selected the option. If you want the center for rotation to

stay at the center of the Workspace, reset the view first, then select the option. 

If you want to display the center for rotation, select 

Display center of rotation

 in the 

Workspace

tab of the 

Preferences

 panel.

4.3

Saving, Restoring, and Managing Views

When you have set up the view of the Workspace for a particular purpose—for example, with a

particular view of a binding pocket—you can save the view for future use. Views can be saved

with a name, restored, and even played through. The tools for working with views are available

from the 

View

 menu and the 

Saved Views

 toolbar, which you display by choosing 

Window 

→

Toolbars 

→

 Saved Views

, or by clicking the 

Saved Views

 button on the 

Manager

 toolbar. The

toolbar buttons are described below. 

Save 

Save the current view of the Workspace (orientation, location, and zoom) as a saved view. 

Opens a dialog box in which you can name the view.

Menu equivalent: 

View 

→

 Save

.

Previous 

Apply the previous view in the list of saved views to the Workspace. 

Menu equivalent: 

View 

→

 Restore View 

→

 Previous

.

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