Chem3D Users Manual - CambridgeSoft

If you select four contiguous atoms the dihedral
angle appears in the model label. If you select two
bonded or non-bonded atoms, the distance
between those atoms appears.
To specify what information appears in atom,
bond, and angle labels:
• In the Model Settings dialog box, select the
Pop-up Info tab, then select the information you
want to display.
Atom Types
Atom types contain much of the Chem3D chemical
intelligence for building models with reasonable 3D
geometries. If an atom type is assigned to an atom,
you can see it in the model data when you point to
it. In the previous illustration of pointing
information, the selected atom has an atom type of
“C Alkane”.
An atom that has an atom type assigned has a
defined geometry, bond orders, type of atom used
to fill open valences (rectification), and standard
bond length and bond angle measurements
(depending on the other atoms making up the
bond).
The easiest way to build models uses a dynamic
assignment of atom types that occurs as you build.
For example, when you change a single bond in a
model of ethane to a double bond, the atom type is
automatically changed from C Alkane to C Alkene.
In the process, the geometry of the carbon and the
number of hydrogens filling open valences changes.
You can also build models without assigning atom
types. This is often quicker, but certain tasks, such
as rectification or MM2 Energy Minimization, will
also correct atom types because atom types are
required to complete these tasks.
To assign atom types as you build:
• In the Chem3D Model Settings dialog box,
select the Model Build tab, then check the
Correct Atom Types checkbox.
To assign atom types after building:
• Select the atom(s) and use the Rectify command
on the Structure menu.
Atom type information is stored in the Atom Types
table. To view the Atom Types table:
• From the View menu, select Parameter Tables,
then select atom types.xml.
Rectification
Rectification is the process of filling open valences
of the atoms in your model, typically by adding
hydrogen atoms.
To rectify automatically as you build, do the
following:
• In the Chem3D Model Settings dialog box,
select the Model Build tab, and then check the
Rectify checkbox.
If you activate automatic rectification in the Model
Settings dialog box, you have the option of showing
or hiding hydrogens. If you turn off automatic
rectification, the Show Hs and Lps command on the
Model Display submenu of the View menu is
deactivated, and you will not have the option of
displaying hydrogens.
Bond Lengths and Bond Angles
You can apply standard measurements (bond
lengths and bond angles) automatically as you build
or apply them later . Standard measurements are
determined using the atom types for pairs of
bonded atoms or sets of three adjacent atoms, and
are found in the external tables Bond Stretching
Parameters.xml and Angle Bending Parameters.xml.
The Model Explorer
The Model Explorer allows users to explore the
hierarchical nature of a macromolecule and alter
properties at any level in the hierarchy. Display
ChemOffice 2005/Chem3D Chem3D Basics • 27
Model Building Basics