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When you delete atoms, the terminal atoms that are attached to this atom can be deleted, or the

terminal atoms can be left in place. Terminal atoms are atoms that are bonded only to that

atom, such as hydrogen or a halogen. Deleting terminal atoms would not, for example, delete a

methyl group attached to the deleted atom. This action is controlled by an option that you can

set in the 

Builder

 tab of the 

Preferences

 panel. 

Another means of deleting atoms is to select them and choose 

Edit 

→

 Cut

 or press 

CTRL+X

.

The atoms are removed from the structure and placed on the clipboard. You can then paste

these atoms into the Workspace later, as a scratch entry.

If you want to remove all atoms in the Workspace, choose 

Workspace 

→

 Clear

 or use the 

Clear

Workspace

 button, which is located on the main toolbar. This action does not delete the atoms

from the structure, it only removes them from the Workspace.

If you want to delete bonds, either to create new ones or to split a molecule into smaller pieces,

you can, you can right-click and hold on a bond in the Workspace and choose 

Delete

 from the

shortcut menu, or choose 

Bonds

 from the 

Delete

 button menu on the 

Edit

 toolbar or the 

Build

toolbar, then click on the bond to delete.

Zero-order bonds are a special type of bond that are used to define connectivity when a frag-

ment “belongs” to a molecule. Two fragments that are joined by a zero-order bond are consid-

ered to be a single molecule in Maestro. One instance where zero-order bonds are used is for a

metal atom in a complex, where for purposes of force-field calculations it must be treated as an

ion, but for purposes of connectivity it is considered part of the complex. You can delete zero-

order bonds in the same way as regular bonds, and you can delete all zero-order bonds by

choosing 

Zero Order Bonds

 from the 

Delete

 button menu.

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Chapter 6

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Maestro User Manual

Chapter 6:

Selecting Atoms

Maestro has a powerful set of tools for selecting atoms in a structure: toolbar buttons, picking

tools in panels, and the 

Atom Selection

 dialog box. These tools allow you to select atoms in two

ways:

• Select atoms first and apply an action to them

• Choose an action first and then select atoms for that action

6.1

Picking in the Workspace

One of the primary means of selecting atoms is to pick atoms in the Workspace. The tools with

which you can do so are described in later sections. To pick an atom, you click on the atom.

The atom is then selected. If you want to select multiple atoms, you can drag over the region

containing those atoms, and they are all selected. If you want to add atoms to the selection,

hold down 

SHIFT

 while you click or drag. To invert the selection of atoms (select the

unselected atoms, deselect the selected atoms), hold down 

CTRL

 while you click or drag. If

you click or drag in an empty part of the Workspace, the selection is cleared. Dragging over

ribbons when the associated atoms are not displayed selects the associated atoms inside the

rectangle. 

The Selection shortcut menu also has some items for selecting atoms. You can invert the selec-

tion, and you can extend the selection to atoms within a radius or atoms that match by color,

representation, or element. See 

Table 2.2 on page 28

 for information on this shortcut menu.

6.2

Using the Toolbar Buttons

The small triangle in the lower right corner of a toolbar button indicates that the button

contains a menu. Many of these buttons allow you to choose a structural unit for selecting.

Choose 

Atoms

, 

Bonds

, 

Residues

, 

Chains

, 

Molecules

, or 

Entries

, then click on an atom in the

Workspace to perform the action on all the atoms in that structural unit. 

For example, to select atoms in residues with the 

Select 

button:

1. Choose 

Residues

 from the 

Select 

button menu:

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The button changes to:

2. Click on an atom in a residue in the Workspace to select all the atoms in that residue.

The 

Select 

button is the primary means of selecting atoms in the Workspace prior to

performing an action. 

In addition to selecting atoms by picking, you can expand the selection to include atoms within

a given distance of the current selection. To include all atoms in residues that have any atoms

within the specified distance, select 

Expand Residues

 on the 

Select 

button menu. If this option

is not selected, only the atoms within the specified distance are added. To expand the selection,

choose the distance from the 

Select 

button menu, or choose 

Custom

 and enter the distance in

the dialog box that opens.

If you want to replace the selection with the atoms within a given distance of the selection,

select 

Exclude Selected

 from the 

Select atoms 

button menu. This is useful if, for example, the

ligand is selected, and you want to select the receptor residues that are within a given distance

of the ligand, but not include the ligand in the selection.

These tools are also available from the 

Expand Selection

 submenu of the Selection shortcut

menu (see 

Section 2.7 on page 26

).

If you want to select all atoms in a particular category, you can choose the category from the

Select

 button menu. The available categories are:

•

All

—all atoms 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. 

•

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.

•

All Hydrogens

—all hydrogen atoms. 

•

Nonpolar Hydrogens

— hydrogen atoms bonded to carbon. 

•

Nonpolar Ligand Hydrogens

— hydrogen atoms bonded to ligand carbon atoms. 

•

Polar Hydrogens

— hydrogen atoms bonded to atoms other than carbon. 

•

Membrane

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

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