Maestro User Manual

Chapter 6: Selecting Atoms

Maestro 10.2 User Manual

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These categories are available on other toolbar buttons that allow you to pick atoms.

6.3

Using the Picking Tools

The picking tools are embedded in each panel in which you need to select atoms to apply an

operation. The picking tools in a panel can include one or more of the following:

•

Pick

 option menu—Allows you to choose a structural unit for selecting atoms. The pick

option menu is described on 

page 123

.

•

Dihedral

 button—Opens the 

Dihedral Selection

 dialog box, in which you can select pro-

tein dihedral angles. 

•

Markers

 option—Marks the selected atoms in the Workspace 

• Text box—Allows you to type in an ASL expression, and displays the ASL expression for

the current selection. ASL stands for Atom Specification Language, and is described in

detail in the 

Maestro Command Reference Manual

. 

•

Clear

 button—Clears the current selection. This button is displayed in the text box when

an expression is present.

•

All

 button—Selects all atoms in the Workspace. This includes atoms that are not dis-

played.

•

Atom Selections 

button—This button displays a list of common atom categories that can

be selected when you click it. Clicking one of the items acts on the corresponding atoms,

if the action is immediate, or adds the atoms to the selection, if the action is performed

later. It also has two buttons, to build or recall atom selections using ASL expressions. 

The atom categories that you can act on or add to the selection are: 

•

Workspace Selection

—atoms that are already selected in the Workspace.

•

Displayed Atoms

—atoms that are displayed in the Workspace. 

•

Protein

—protein atoms (backbone and side chain).

•

Protein Backbone

—protein backbone atoms. 

•

Protein Side Chains

—protein side chain atoms. 

•

Protein Near Ligand

—protein residues within 5 Å of the ligand. 

•

Ligands

—ligand atoms, as defined in the 

Ligand Detection Settings

 dialog box. 

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Chapter 6: Selecting Atoms

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122

•

Waters

— all water molecule atoms.

•

Ions

— charged atoms and molecules that have less than 10 atoms.

•

Metals

—all elements to the left of B, Si, Ge, Sb, Po in the periodic table.

•

Heavy Atoms

—all non-hydrogen atoms.

•

Hydrogens-All

—all hydrogen atoms. 

•

Hydrogens-Nonpolar

— hydrogen atoms bonded to carbon. 

•

Hydrogens-Nonpolar Ligand

— hydrogen atoms bonded to ligand carbon atoms. 

•

Hydrogens-Polar

— hydrogen atoms bonded to atoms other than carbon. 

•

Membrane

—atoms in membrane molecules (POP, POPC, POPE, DPPC, DPMC).

These are the same as on the 

Select

 button menu (and other button menus), except for the

first item.

The two buttons are:

•

Select

—Opens the 

Atom

 

Selection

 dialog box (see 

Section 6.5 on page 125

)

•

Previous

—Performs the action on the most recent atom selection defined in the

Atom Selection

 dialog box (see 

Section 6.5 on page 125

). 

The range of picking tools available in a panel varies according to the types of structural units

that are needed for the operation and whether picking causes immediate action or requires an

action to be specified later. The ASL text box and 

Clear

 button are included only when picking

merely defines a set of atoms for later use. For example, the 

Dihedral

 tab of the 

Adjust 

panel

has a 

Pick

 option menu and a 

Dihedral

 button, and the action is immediate. The 

Sets

 panel has

a full set of picking tools, and stores the atoms in a defined set that can be used later. When

picking for an action to be performed later, each picking action adds atoms to the ASL expres-

sion (with an implicit OR), which is (with an implicit OR) shown in the ASL text box. 

Figure 6.1. Examples of picking tools. Top: from the Sets panel; Center: from the Atom 

and Bond Coloring panel; Bottom: from the Adjust panel.

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Chapter 6: Selecting Atoms

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6.3.1

The Pick Option Menu

With the 

Pick

 option menu, you can choose a structural unit (

Atoms

, 

Bonds

, 

Residues

, 

Chains

,

Molecules

, or 

Entries

) and click on an atom or a bond in the Workspace to select all the atoms

in that structural unit. For instance, choose 

Atoms

 and click on an atom in the Workspace to

select just that atom. Choose 

Residues

 and click on an atom to select all the atoms in that

residue. Choose 

Bonds

 and click on a bond to select both atoms that define that bond. 

Figure 6.2. The Sets panel, showing the Pick option menu.

When you select a structural unit, the cursor in the Workspace appears as a box with a letter: A,

B, R, C, M, and E represent 

Atoms

, 

Bonds

, 

Residues

, 

Chains

, 

Molecules

, and 

Entries

, respec-

tively. Successive clicks add atoms to the selection.

If you want to know the index of structural unit that you are picking (for example, the molecule

number), you can set a preference to show the index in the status bar. When the pointer is over

an atom, the index of the structural unit is displayed as Pick:  index at the beginning of the

status bar. See 

Section 14.5.1 on page 358

 for details on the preference.

The number of structural units available in the menu depends on the operation. For instance,

when you define a dihedral angle, you can pick either four atoms or three bonds. The 

Pick

option menu for this operation therefore only contains 

Atoms

 and 

Bonds

.

You do not need to select the 

Pick

 option before choosing an item from the 

Pick

 option menu; it

is automatically selected when you choose a menu item.

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