Chem3D Users Manual - CambridgeSoft

Any atoms that fall at least partially within the
Selection Rectangle are selected when you release
the mouse button. A bond is selected only if both
atoms connected by the bond are also selected.
To keep previously selected atoms selected:
• Hold down the Shift key while you make
another selection.
If you hold down the Shift key and all of the
atoms within the Selection Rectangle are
already selected, then these atoms are
deselected.
Defining Groups
You can define a portion of your model as a group.
This provides a way to easily select and to highlight
part of a model (such as the active site of a protein)
for visual effect.
To define a group:
1. Select the atoms and bonds you want in the
group. Using the select tool, select the first
atom then use Shift+click to select the other
atoms and bonds.
2. While still pointing at one of the selected
atoms, right-click and choose New Group from
the Context-Sensitive menu.
If the groups in your model are substructures
defined in the Substructures table
(substructures.xml), you can assign standard colors
to them.
To assign (or change) a color:
1. From the View menu, point to Parameter tables
and select Substructures.
2. Double click in a cell in the Color field.
The Color dialog box appears.
3. Select a color and click OK.
4. Close and Save the Substructures table.
Once colors are assigned in the Substructures table,
you can use them to apply color by group:
1. From the File menu, choose Model Settings.
2. Select the Model Display control panel.
3. Select the Group radio button in the Color by
section.
Each atom in your model appears in the color
specified for its group.
NOTE: Color by Group is only displayed when Ribbon or
Cartoon display mode is selected.
Selecting a Group or Fragment
There are several ways to select a group or
fragment. The simplest is to use the Model
Explorer, and select the fragment.
selects the entire chain
You may also select a single atom or bond and use
the Select Fragment command on the Edit menu.
NOTE: If you want to select more than one fragment, you
must use the Model Explorer.
ChemOffice 2005/Chem3D Manipulating Models • 93
Selecting