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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.