Maestro User Manual

Chapter 6: Selecting Atoms

Schrödinger Software Release 2015-2 

124

6.3.2

The Dihedral Selection Dialog Box

For proteins, you can select the dihedrals by name in the 

Dihedral Selection

 dialog box, which

you open by clicking the 

Dihedral

 button in the picking tools.

Figure 6.3. The Dihedral Selection dialog box.

To select one or more dihedral angles:

1. Select one or more chains in the 

Entry (Chain)

 list.

The list of residues in the selected chains is displayed in the 

Residues

 list.

2. Select one or more residues in the 

Residues

 list.

3. Select the dihedrals in the 

Dihedrals

 list.

The dihedrals are selected for each selected residue, and the number of dihedrals is displayed

below the table. If 

Show markers

 is selected, the dihedrals are marked in the Workspace. 

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6.4

Using the Edit Menu

The 

Edit

 menu also has a set of tools for picking atoms, on the 

Pick

 and 

Select Atoms

submenus. You can choose the structural unit to pick from the 

Pick

 submenu, which also sets

the structural unit on the 

Select atoms

 toolbar button menu. To pick atoms, choose 

Edit 

→

Select Atoms 

→

 Pick to Select

, which is the same as clicking the 

Select atoms

 toolbar button,

or pressing the 

`

 key (backquote). 

In addition to selecting atoms by picking, the 

Select Atoms

 submenu has items to select all

atom (

All

), clear the selection (

None

), invert the selection (

Invert

), select the previous or next

residue (

Previous

/

Next

), or open the 

Atom Selection

 dialog box.

6.5

The Atom Selection Dialog Box

If you want to make atom selections based on more complex criteria, such as selecting all the

carbon atoms in a protein backbone, you can use the 

Atom Selection

 dialog box. The 

Atom

Selection

 dialog box allows you to select atoms by defining complicated ASL expressions

without the need to understand the ASL syntax.

Figure 6.4. The Atom Selection dialog box.

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Chapter 6: Selecting Atoms

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To open the 

Atom Selection

 dialog box, choose 

Select

 from a button menu or click 

Select

 in the

picking tools of a panel. The 

Atom Selection

 dialog box is modal: you must dismiss it before

you can perform any other operations, with the exception of rotation and translation of struc-

tures and selecting atoms in the Workspace. 

When you close the 

Atom Selection

 dialog box, the ASL expression is automatically stored and

can be recalled with the 

Previous

 button on any set of picking tools.

To select atoms

1. Create an atom group by selecting a property and value (see 

Section 6.5.1 on page 126

).

2. Click 

Add

 or 

Subtract

 to define the current selection (see 

Section 6.5.4 on page 127

).

3. Create more atom groups as needed and click 

Add

, 

Subtract

, or 

Intersect

 to modify the

current selection (see 

Section 6.5.4 on page 127

).

4. When you are satisfied with the current selection, click 

OK

 to apply the operation to the

selection. 

Some operations, such as deleting atoms, take effect immediately. Others merely define a set of

atoms to be used in a subsequent task, such as selecting atoms for creation of a surface. 

The features of the 

Atom Selection

 dialog box are described in the following sections.

6.5.1

Selecting Atoms by Property

You can create an atom group by selecting a property and a value for that property. These prop-

erties are grouped into a number of categories, each in their own tab: 

Atom

, 

Residue

, 

Molecule

,

Chain

, and 

Entry

. For each category there is a list of properties shown on the left of the tab,

from which you can select one item. When you select an item, tools for that property are

displayed in the center of the tab. The three types of tools are:

• Text box. You can specify the allowed values for the property by using lists of numbers,

closed ranges (e.g. 12-42) and open ranges (e.g. >= 30). 

• List. You can choose one or more entries from the list by clicking, in combination with

the 

SHIFT

 and 

CTRL

 keys. Only items that are currently in the Workspace are displayed

in the list.

• Set of options, which can be nested. You can choose only one of the possible combina-

tions by selecting the options.

With text boxes and lists, you can also choose items by selecting atoms in the Workspace. For

example, if you choose the 

Element

 property in the 

Atom

 category, then select a carbon atom in

the Workspace, the “C” item in the list of elements is selected. 

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