Maestro User Manual

Chapter 6: Selecting Atoms

Maestro 10.2 User Manual

129

Figure 6.5. The Proximity dialog box.

You can either include or exclude the source atoms in the selection. For example, you might

want to include residues within a certain distance of a metal atom, but not include the atom

itself. The 

Update Markers

 button updates the markers for the proximity selection so that you

can view the selection in the workspace before accepting it.

6.5.6

Editing and Storing Expressions

You can undo multiple operations with repeated clicks on the 

Undo

 button. The 

Redo

 button

reverses undo operations, and can also be used multiple times. (These are the buttons in the

dialog box, not the toolbar button.)

You can also type ASL expressions directly into the 

ASL

 text box. The hand-edited expressions

are considered part of the last operation performed with the mouse and can be undone and

redone as part of that operation, but cannot be undone or redone separately.

The 

Create Set

 button opens a dialog box that enables you to name and store the existing ASL

expression for use as a set definition. The sets created in this manner are the same as sets

created with the 

Sets

 panel, and are listed in the 

Set

 tab. You can therefore create sets from the

Atom Selection

 dialog box, and use them for atom selection later. For more information on

creating and saving sets, see 

Section 10.4 on page 259

.

6.5.7

Converting Expressions to Lists

ASL expressions are stored as formal expressions that can be applied in different contexts to

select different sets of atoms. If you want an expression that explicitly lists the atom numbers

or the residue numbers, you can convert the ASL expression in the 

ASL

 text box into a list of

atoms by clicking 

Atom Num

, or into a list of residues by clicking 

Res Num

. 

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Chapter 6: Selecting Atoms

Schrödinger Software Release 2015-2 

130

6.5.8

Examples of Atom Selection

Below are some examples of the use of the 

Atom Selection

 dialog box. It is assumed that you

have the 

Atom Selection

 dialog box open. To apply your selection and dismiss the dialog box,

click 

OK

. These examples assume that the protein and the ligand are in separate entries in the

Workspace.

To select all carbon atoms in the backbone of a protein:

1. In the 

Atom

 tab, select 

Element

 from the list of properties.

2. Select 

C

 from the list of elements.

3. Click 

Add

 to add the atom group to the ASL expression.

4. Select 

Backbone/Side Chain

 from the list of properties.

5. Select the 

Backbone

 option.

6. Click 

Intersect

 to restrict the current ASL expression to be applied only to protein back-

bone atoms.

If you want to continue to the next example, click 

Clear

 to clear the current ASL expression.

To select all side chains within 5.0 Å of a ligand in the active site of a ligand/receptor 

complex:

1. In the 

Entry

 tab, select the entry name for the ligand from the list of entries.

2. Click 

Add

 to make this entry name the current ASL expression.

3. Click 

Proximity

 to open the 

Proximity

 dialog box 

4. Enter 5.0 in the text box, click 

Residues

 in the 

Fill

 section, select 

Exclude source

, then

click 

OK

.

5. In the 

Residue

 tab, select the 

Backbone/Side Chain

 property.

6. Select the 

Sidechain

 option.

7. Click 

Intersect

 to restrict the current ASL expression to include only atoms in the protein

side chain.

8. If you want to continue to the next example, click 

Clear

 to clear the current ASL expres-

sion.

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To select a range of residues but exclude proline residues:

1. In the 

Residue

 tab, select 

Sequence

 from the property list.

2. Select the appropriate chain from the list of chains in the top scrolling list.

3. Select a range of residues in that chain from the lower scrolling list.

4. Click 

Add

 to make this residue range the current ASL expression.

5. Select the 

Residue Type

 property.

6. Select 

PRO

 from the list of residue types.

7. Click 

Subtract

 to exclude proline residues from the current ASL expression.

6.6

Storing the Workspace Selection

When you have made an atom selection, you can also store the selection in a memory location.

To do so, ensure that the pointer is in the Workspace, then press 

CTRL+

numeral-key (for

example, 

CTRL+3

), or choose 

Edit 

→

 Select Atoms 

→

 Save 

→

 Selection 

number. The selec-

tion is stored in the memory location corresponding to the numeral key or number. To retrieve

the selection, simply press the numeral key when the pointer is in the Workspace, or choose

Edit 

→

 Select Atoms 

→

 Restore 

→

 Atom Selection 

number. 

Selections are stored as an ASL expression that consists of the atom numbers relative to the

Workspace of the selected atoms. When you change the contents of the Workspace, the atom

numbers can change. If you retrieve a selection from memory after changing the Workspace

contents, the selection is applied to the current atom numbering, and might result in a selection

that is different from what you expected. However, if you replace the Workspace contents with

a conformer of the previous contents, for example, the stored atom selections should apply to

the corresponding atoms in the conformer.

For a more general storage facility, you can create atom sets in the 

Sets

 panel. See 

Section 10.4

on page 259

 for more information. These stored selections are not the same as the named atom

sets, as they can only be defined and used in the Workspace. 

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