Maestro User Manual

Chapter 5: Building and Adjusting Structures

Maestro 10.2 User Manual

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3. Edit the table cells to change the property values:

• To change a property for a single atom, simply edit the table cell. 

• To set the value for multiple atoms, select the atom rows in the table, edit one of the

table cells, and press 

CTRL+ENTER

 to apply the change to the selected rows.

Selecting atoms in the table also selects them in the Workspace.

To delete property values for all atoms in the Workspace:

1. Choose the properties from the 

Properties

 list. 

2. Click 

Delete

. 

The property values are removed from all atoms in the Workspace (not just those in the

table), and the property is removed from the 

Atoms

 table.

To add a property to the atoms that are selected in the Atoms table:

1. Click 

Add

. 

The 

Add Property

 dialog box opens. 

2. Select the property type, name the property, and provide an initial value. 

3. Click 

OK

. 

The property is added as a column to the 

Atoms

 table, and the values are added to the

selected atoms.

5.12 Changing Residue Properties

Residue properties can be changed in the 

Residue Properties

 tab. This tab is laid out in a

similar fashion to the 

Atom Properties

 tab, with a 

Property

 option menu and a set of tools

displayed for each choice. The residue properties and their tools are described below. In order

to view the results, you must first display the appropriate atom labels. 

Residue Number

To renumber more than one residue by incrementing the residue numbers, you can use the

Renumber Residues

 section. Enter the starting value in the 

Renumber From

 text box, then use

the picking tools to select the residues to renumber. The residue with the lowest number in the

selection is assigned the number in the text box. The residue numbers for the remaining resi-

dues are shifted by the same amount as that of the residue with the lowest number. Renum-

bering therefore preserves gaps in the residue numbering. If you want to eliminate gaps, select

the residues above the gap and renumber them.

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Figure 5.16. The Residue Number tools in the Residue Properties tab.

Renumbering a single residue is the same as assigning its number. To apply a specific residue

number to one or more residues, in the A

pply residue number

 section enter the number you

want to apply in the 

Residue number

 text box, then use the picking tools to select the residues

to apply the number to. You can also reassign the residue number of single atoms whose

number is misassigned with these tools, by selecting 

Atoms

 from the 

Pick

 option menu, then

picking the atom to assign the specified residue number.

Residue Name

To name residues, enter the residue PDB name in the 

Residue PDB name

 text box, and use the

picking tools to select the residues to name. PDB residue names are three characters long and

are right-justified. For example, the residue name G3 must be entered with a leading space, as

“ G3”, whereas the residue name C19 should have no leading space, “C19”. 

Chain Name 

You can assign a single-letter name to chains. The definition of a chain is not restricted to the

items labeled 

Chain

 in the pick option menus: you can define a chain in any way that you like,

and assign it a name. To assign the name, enter a character in the 

Chain Name

 text box and use

the picking tools to select the chain. To remove a chain name, clear the 

Chain Name

 text box

and use the picking tools to select the chain.

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5.13 Defining Dummy Atoms

Dummy atoms are used by several of the computational programs for defining geometries and

geometric parameters. You can retype an atom to a dummy atom type using the 

MacroModel

Types

 atom property described earlier. You can also place a dummy atom at the centroid (mean

position) of a group of atoms, such as a ring. You can then change the dummy atom to a real

atom, and thus place real atoms at the centroid of some system of interest. 

The centroid capability is available in the 

Centroids

 panel, which you open from the 

Edit

 menu,

and is docked into the Workspace by default. To define a centroid, use the picking tools in the

Define atoms for centroid

 section. The atoms are listed in the 

Atoms to define centroid

 list. If

you have 

Markers

 selected, the atoms are marked with a salmon-colored star, and the atom that

is selected in the list is marked with a lavender-colored star. You can delete atoms from the list

by selecting the list item and clicking 

Delete

. Once you have picked all the atoms, click 

Create

Centroid Atom

. The To define another centroid, click 

Delete All

 before picking atoms for the

new centroid. 

Figure 5.17. The Centroids panel.

5.14 Deleting Atoms and Bonds

If you need to delete atoms from a structure, you can use the 

Delete

 submenu of the 

Edit

 menu

or the 

Delete

 button menu on the 

Edit

 toolbar or the 

Build

 toolbar.

These menus offer choices for the type of object to delete, and allow you to open the 

Atom

Selection

 dialog box to select atoms for deletion based on their properties. You can also select

atoms in the Workspace, then click the 

Delete

 button, press 

DEL

, or use the shortcut menu to

delete them. 

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