Maestro User Manual

Chapter 5: Building and Adjusting Structures

Schrödinger Software Release 2015-2 

100

When you click the last atom, the distance is highlighted with two yellow solid lines, a

purple dotted line, and an arrow indicating the direction of adjustment. Angles are high-

lighted in green and orange, and dihedrals are highlighted in red and turquoise.

3. With the left mouse button, drag to the right to increase the distance or to the left to

decrease it. Alternatively, use the scroll wheel or the pinch gesture to adjust the distance.

You can choose bond lengths or dihedrals for adjustment by right-clicking on a bond in the

Workspace and choosing 

Distance

 or 

Dihedral

 from the 

Adjust

 submenu on the shortcut menu.

For a faster adjustment of a dihedral, choose 

Quick Torsion

 from the 

Adjust 

button menu, click

on a bond, then drag with the left mouse button. The fragment that is rotated has an arrow

pointing to it on the end of the bond nearest the moving fragment. By default the smaller frag-

ment is rotated around the selected bond. To change the fragment that is rotated, click the bond

again. 

Quick Torsion

 is selected by default, so if you have not previously selected some other

adjustment, you only need to click on the 

Adjust

 button, then perform the adjustment. 

If you want to display interactions such as hydrogen bonds and contacts while adjusting struc-

tures, you can select 

Display Interactions

 from the 

Adjust 

button menu. The interactions that are

displayed can be set as preferences—see 

Section 14.8.2 on page 365

 for more information. 

5.9.1.2

From the Adjust Panel

The tools for adjusting bond lengths, bond angles, and dihedral angles are similar, so the

description given here is generic.

Figure 5.7. The Adjust panel, showing the Dihedral tab.

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Chapter 5: Building and Adjusting Structures

Maestro 10.2 User Manual

101

To define the geometric parameter that you want to adjust, choose 

Atoms

 or 

Bonds

 from the

Pick

 option menu in the 

Define atoms for

 operation section, and pick the atoms or bonds. For a

bond length, you must pick two atoms or one bond; for a bond angle, you must pick three

atoms or two bonds; for a dihedral angle you must pick four atoms or one bond—the bond

about which the rotation is performed. When you pick this bond, the groups attached to the

atom nearest the point you click are the ones that are moved.

In addition to the standard picking tools just described, you can also specify dihedrals in

proteins using standard names (psi, phi, omega, etc.). Click 

Select

 in the 

Dihedral

 tab and

select dihedrals by the residues in each entry (or chain), or by standard names.

The atom numbers of the selected atoms are listed in the table in the center of the tab. The last

atom that you pick is the “target atom”—the atom that is moved in the adjustment process. You

must also decide which of the attached atoms to move along with the target atom. You can

choose from 

All attached atoms

, 

All attached terminal atoms

, or 

Only single atom

. If the target

atom is part of a ring, the first option is unavailable. 

Once you have chosen the atoms for a particular adjustment, you can make the adjustment by

dragging with the left mouse button, by using the scroll wheel, or by entering a new value for

the geometric parameter in the 

Current

 column of the table. If you enter a new value, the value

is changed and the Workspace is updated when you press 

ENTER

. You can make adjustments

using the table at any time, but you can only use the mouse immediately after picking. 

5.9.1.3

Repeating Adjustments

When adjusting a structure, you might want to switch between adjusting two or more parame-

ters. If the parameters are of the same type, you can select the previous or the next adjustment

by choosing 

Edit 

→

 Adjust 

→

 Previous Adjustment

 or 

Edit 

→

 Adjust 

→

 Next Adjustment

, or use

CTRL+SHIFT+A

 

(



Z

) and 

CTRL+SHIFT+Z

 

(



Z

). If they are of different types, you can

select the adjustment type again, using the 

Edit

 menu or the 

Adjust

 button, and the last adjust-

ment of that type made is selected. You can also select the adjustment you want to change in

the 

Adjust

 panel, by selecting the table row in the tab for the adjustment type. 

5.9.2

Adjusting Peptide Linkages and Side Chains

The 

Adjust

 button menu on the main toolbar provides some tools for adjusting the geometry of

peptide linkages, and for selecting the most common rotamers for side chains. 

For peptide linkages, you can rotate the plane of the peptide linkage, rotate the carbonyl plane,

and convert between cis and trans linkages. 

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