Maestro User Manual

Chapter 6: Selecting Atoms

Maestro 10.2 User Manual

127

The current atom group is represented in two ways: the atoms are marked in purple in the

Workspace (if 

Show markers

 is selected) and the value in the 

Atoms Matching

 field indicates

how many atoms are matched by the current property specification.

6.5.2

Selecting Atoms by Connectivity 

You can create an atom group by specifying a substructure in the 

Substructure

 tab that defines

the connectivity of the atoms. This is a convenient way of selecting all instances of a particular

functional group, for example.

Maestro provides access to two substructure notations, SMARTS, and Maestro. The Maestro

substructure notation is described in 

Appendix C

, and is similar to SMARTS. To select atoms

that match a particular substructure, type the pattern for the substructure in the text area. If you

select SMARTS notation, you can automatically generate the pattern from the Workspace

selection by clicking 

Get From Selection

. You can make the selection in the Workspace while

the 

Atom Selection

 dialog box is open. A SMARTS pattern that matches the selection replaces

the content of the text area. If there are many atoms in the Workspace, it may take some time.

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

Section 14.15 on page 382

.

6.5.3

Selecting Atoms Using Previously Defined Sets or Selections

In the 

Sets

 tab, you can select atom sets that have been defined previously. Maestro provides a

list of predefined atom sets. You can also define your own sets, either directly in the 

Sets

 panel,

or by using the 

Atom Selection

 dialog box to select the atoms, then clicking 

Create Set

. These

named sets are stored with the project and are available in the 

Sets

 tab. The sets are stored as

ASL expressions, unless you convert them to a list of atom or residue numbers. They can there-

fore be transferred from one structure to another. You can use the 

Sets

 panel to select atoms in

any of the sets you have created—see 

Section 10.4 on page 259

 for details.

There are two other ways of recalling a previously defined atom selection. The first is to click

Previous

 (below the 

ASL

 text box), which recalls the atom selection defined the last time the

Atom Selection

 dialog box was used. The second is to click 

Selection

, which uses the atoms

that are selected in the Workspace as the ASL expression. Both of these buttons replace the

current ASL expression: any existing expression is lost. You can add to these expressions, so

they are useful as a starting point for a more complex expression. 

6.5.4

Combining and Modifying Atom Selections

Once you have created an atom group, you can combine it with the current selection. The 

Add

,

Subtract,

 and 

Intersect

 buttons combine the ASL expression for the atom group with the

existing ASL expression in the 

ASL

 text box (the current selection), as follows: 

---

Chapter 6: Selecting Atoms

Schrödinger Software Release 2015-2 

128

• The 

Add

 button includes the atom group in the current selection by performing a boolean

OR operation on the ASL expressions. 

• The 

Subtract

 button excludes the atom group from the current selection by performing a

boolean AND NOT operation on the ASL expressions. 

• The 

Intersect

 button restricts the selection to the atoms that are in both the atom group

and the current selection by performing a boolean AND operation on the ASL expres-

sions. 

Note:

Intersect

 is not available for the first atom group that is defined.

In addition to combining ASL expressions to modify the current selection, you can use the

following buttons:

•

All

—select all atoms in the Workspace. Replaces the existing expression.

•

Undo

—undo the last operation

•

Redo

—redo the last operation

•

Clear

—clear the ASL expression 

•

Invert

—negate an entire expression

•

Previous

—recall the atom selection defined the last time the 

Atom Selection

 dialog box

was used. Replaces the existing expression.

•

Selection

—use the atoms that are selected in the Workspace as the ASL expression.

Replaces the existing expression.

•

Atom Num

—convert the ASL expression to list each atom explicitly by atom number

•

Res Num

—convert the ASL expression to list each residue explicitly by residue number

If 

Show Markers

 is selected, the atoms corresponding to the current selection (the expression in

the ASL text box) are highlighted with light blue markers in the Workspace.

6.5.5

Selecting Atoms by Proximity

Once you have made an initial selection, you can select atoms based on their distance from the

atoms defined by the current ASL expression (the source atoms) in the 

Proximity

 dialog box,

see 

Figure 6.5 on page 129

. To open this dialog box, click 

Proximity

.

You can specify the distance in angstroms or in terms of the number of bonds. If the boundary

for inclusion intersects a molecule or a residue, you can choose to include the entire molecule

or residue using the 

Fill

 buttons. 

---