Maestro User Manual

Chapter 5: Building and Adjusting Structures

Maestro 10.2 User Manual

105

Figure 5.9. The Advanced Transformations panel.

To transform the selected atoms:

1. Select the atoms in the Workspace.

2. Right-click in the Workspace and choose 

Transform

.

3. Rotate or translate the atoms with the right or middle mouse button.

To transform atoms by picking:

1. Enter local transformation mode by one of the following methods:

• Choose 

Edit 

→

 Transform 

→

 Pick to Transform

.

• Select 

Local

 for 

Rotation/translation scope

 in the 

Advanced Transformations

 panel.

• Click the 

Transform

 toolbar button.

2. Choose a type of structure to pick:

• Choose 

Edit 

→

 Pick 

→

 

type. 

• Choose from the 

Pick

 menu in the 

Atoms for Transformation

 section of the 

Advanced

Transformations

 panel.

• Select the type from the 

Transform

 button menu.

3. Pick the atoms in the Workspace.

You can drag to pick multiple structural objects, but you can only pick once—you cannot

add to the selection. 

4. Rotate or translate the atoms with the right or middle mouse button.

Various markers are available to help in the transformation process. These markers can be

turned on and off from the 

Transform

 button menu. If 

Show Markers

  is  selected  from  this

button menu, the picked atoms are marked in yellow, and the rotation center is marked in

magenta. Display of the rotation center is governed by a preference—see 

Section 14.4.4 on

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106

page 350

 for details. You can also display interactions such as hydrogen bonds, contacts, and

bond lengths while you are doing a local transformation. To do so, select 

Display Interactions

or 

Display Bond Lengths

 from the 

Transform

 button menu or the 

Transform

 submenu of the 

Edit

menu. Interactions are displayed between the moving atoms and the remaining atoms. The

interactions that are displayed can be set as preferences—see 

Section 14.8.2 on page 365

 for

more information.

If you want to adjust the view while you are in a transformation, hold down the 

SPACEBAR

and change the view with the mouse buttons. This action temporarily exits local transformation

mode. You can also switch modes in the 

Advanced Transformations

 panel, by selecting 

Global

or 

Local

 under 

Rotation/translation scope

, or by using the shortcut key 

CTRL+G

.

More complex atom selection than a single pick can be done in the 

Atoms for transformation

section of the 

Advanced Transformations

 panel. However, the picking tools in this section still

only allow a single pick. If you have already selected the atoms you want to transform before-

hand, click the 

Atom Selections

 button and choose 

Workspace Selection

. To select more than

one group, choose 

Select

 and use the 

Atom Selection

 dialog box. 

If you want to perform a rotation, a rotation center is required. By default, Maestro selects the

centroid of the atoms selected for transformation as the rotation center. If this is not satisfac-

tory, you must choose a rotation center, which you can do in the 

Advanced Transformations

panel. You can select a new center using the tools in the 

Center for transformation

 section.

Displaying atom number labels may be helpful for determining which atoms you would like to

specify as the rotation center.

When you begin a local transformation, Maestro automatically begins an undo block. As a

result, selecting 

Undo 

action from the 

Edit

 menu reverses all operations that occurred between

the time that the mouse button was pressed, and the time that it was released.

If you are transforming atoms for which some or all of them have alternate positions, you can

transform both alternates by selecting 

Include alternate positions in local transformations

. To

transform only the displayed set of coordinates, deselect this option. This option is also avail-

able in the 

Preferences

 panel.

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Maestro 10.2 User Manual

107

5.9.5

Structure Sculpting

Maestro provides a special mode of local transformation called structure sculpting, which you

enter by choosing 

Structure Sculpting

 from the 

Tools

 menu, or clicking the 

Sculpt

 button on the

Build

 toolbar (also available from the 

Proteins

 toolbar). 

In this mode, the movement of atoms is followed by a short force-field minimization that

includes nearby atoms. Once you enter this mode, you can select atoms and drag them to a new

location (with the left mouse button). When you release the mouse button, the minimization

starts. The selected atoms are restrained. Atoms in the same residues (or molecule, if there are

no residue numbers) have no constraints placed on them; atoms in complete residues that are

within 5 Å of these residues are restrained, and all other atoms are frozen. The minimization

proceeds for a fixed number of cycles (500) or until there is no significant change (maximum

displacement of 0.005 Å). During the minimization you can continue to work on the structure.

The minimization stops if you exit the mode, for example by choosing some other action that

involves picking atoms, or change the content of the Workspace. If you select atoms and drag

them while the minimization is proceeding, it stops and a new minimization begins.

5.9.6

Cleaning Up the Geometry

Maestro provides two tools for cleaning up the structure in the Workspace: the Geometry

Symmetrizer, and the Geometry Cleanup utility. The Geometry Symmetrizer allows you to

symmetrize the geometry of the structure in the Workspace, subject to a given tolerance.

Figure 5.10. The Symmetrize Workspace panel.

To symmetrize the Workspace structure:

1. Choose 

Symmetrize Workspace 

from the 

Edit

 menu. 

The 

Symmetrize Workspace

 panel opens.

2. Click 

Find Point Group

.

The point group found is displayed in the panel.

3. If this is not the desired point group, increase the tolerance and click 

Find Point Group

. 

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