Maestro User Manual

Chapter 3: Importing and Exporting Structures and Data

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62

If you want to use the structure for modeling, you must convert it to a 3D structure, by using

LigPrep for example. The structure retains stereo (R/S or E/Z) properties, which can be used

by LigPrep to ensure the correct stereochemistry. A minimized 3D structure can be generated

when you paste the structure, by choosing 

Edit 

→

 Paste Special 

→

 As 3D

. This feature uses

tools from LigPrep but does not allow any of the flexibility that is available in LigPrep.

You can also copy atoms from a structure in Maestro with 

Edit 

→

 Copy

 or 

CTRL+C (C)

, and

paste them into the Workspace with 

Edit 

→

 Paste

 or 

Edit 

→

 Paste Special 

→

 By Placing

. If

there is nothing in the Workspace, a new entry is created with a default title. If there is a single

entry in the Workspace when you paste, it is added to this entry. If there are multiple entries in

the Workspace when you paste, you are prompted to choose an entry to add the atoms to, or to

create a new entry. When you copy (or cut) the atoms, any bonds between the copied atoms and

the rest of the Workspace structure are broken and capped with hydrogen atoms. You can also

paste the copied structure into ChemDraw.

Another option is to copy atoms as a SMARTS pattern, by selecting atoms in the Workspace

and choosing 

Edit 

→

 Copy as SMARTS

. The SMARTS pattern can then be pasted anywhere

that accepts SMARTS as input—into text boxes in other panels in Maestro, for example. You

can set preferences for some of the notational elements in the SMARTS pattern—see

Section 14.15 on page 382

.

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Chapter 4

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63

Maestro User Manual

Chapter 4:

Viewing the Workspace

The view of the objects in the Workspace can be changed in a variety of ways, and you can

save the view for later use. This chapter describes the different views that are available, how

you can change them, and how you can manage them. It also describes viewing effects such as

tiling, stereo viewing, perspective, and fog. 

4.1

The View Toolbar

The 

View

 toolbar provides tools for changing the view of the Workspace. These buttons are

described briefly below, and in more detail in later sections. See 

Section 2.4 on page 17

 for

general information on toolbars.

Fit 

Fit the selected atoms (or all atoms, if there is no selection) to the Workspace.

Menu equivalent: 

View 

→

 Fit to Workspace 

→

 Selected atoms

.

Fog 

Turn fogging on or off, or select automatic fogging when the Workspace has more than 40 

atoms.

Menu equivalent: 

View 

→

 Fog 

→

 On/Off/Automatic

.

Enhance 

Enhance depth cues.

Menu equivalent: 

View 

→

 Fog 

→

 Enhance Depth Cues

.

Rotate X 

Rotate the Workspace around the x axis by 90 degrees.

Menu equivalent: 

View 

→

 Rotate X 90

.

Rotate Y 

Rotate the Workspace around the y axis by 90 degrees.

Menu equivalent: 

View 

→

 Rotate Y 90

.

Tile 

Arrange the Workspace entries in a rectangular grid of “tiles”. From the button menu you can 

choose to move tiles, transform tiles separately or together, choose how to tile the entries.

Menu equivalent: 

View 

→

 Tile

.

Reset 

Reset the rotation, translation, and zoom of the Workspace to the default state (coordinate x 

and y axes in the plane of the screen, z axis perpendicular to the screen).

Menu equivalent: 

View 

→

 Reset.

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Chapter 4: Viewing the Workspace

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4.2

Changing the View

The view that is presented in the Workspace can be regarded as the image that you see through

a video camera. Changing the view is like moving the camera to a new location or a new angle,

or zooming in or out. Changing the view does not change the coordinates of any of the objects

in the Workspace, it merely changes the camera angle, location, and zoom. However, you can

apply the current view to change the coordinates of the Workspace objects by choosing 

Edit 

→

Update Coordinates

.

The view is stored as a coordinate system, with an origin (location), an orientation (angle), and

a scale factor (zoom). The coordinate system in Maestro is oriented so that the positive z axis

points out of the screen, the x axis is the horizontal axis, and the y axis is the vertical axis. The

default view is the coordinate system and scaling of the structures in the Workspace.

Changing the view is done with a “global transformation” of the coordinate system: a transla-

tion, a rotation, or a zoom. Rotation, translation, and zoom actions are assigned to combina-

tions of mouse buttons with the 

SHIFT

 and 

CTRL

 keys. The default assignments for a 3-button

mouse with a scroll wheel are given in 

Table 4.1

. For information on the mappings for this and

other mouse or trackpad configurations, open the 

Customize Mouse Actions

 panel (

Maestro

 

→

Customize

 

→ 

Mouse Actions

). You should take care that you do not click instead of drag,

because clicking might have a particular action associated with it in the context in which you

are working, and change the structure. The following sections give more details on doing

global transformations. 

Table 4.1. Mapping of Workspace operations to mouse actions.

Operation

Action

Rotate about the x- and y-axes

Drag with middle mouse button

Rotate about the x-axis only

Drag vertically with SHIFT and middle mouse button

Rotate about the y-axis only

Drag horizontally with SHIFT and middle mouse button

Rotate about the z-axis

Drag horizontally with CTRL and middle mouse button

Spot-center on an atom

Right-click

Translate in the x-y plane

Drag with right mouse button

Translate along the y-axis

Drag vertically with SHIFT and right mouse button

Translate along the x-axis

Drag horizontally with SHIFT and right mouse button

Translate about the z-axis

Drag horizontally with CTRL and right mouse button

Zoom

Drag horizontally with middle and right mouse buttons or with 

SHIFT+CTRL and middle mouse button; use the scroll wheel; 

use the pinch gesture.

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