Chapter 3: Importing and Exporting Structures and Data
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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
.
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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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.