Chem3D Users Manual - CambridgeSoft

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Example 2. Building a Model with a
Substructure and Several Other
Elements
To build a model with substructures and other
elements:
1. Type PrNH2 into a text box with no atoms
selected.
2. Press the Enter key.
A model of propylamine appears.
The appropriate bonding site for the Pr
substructure is used for bonding to the
additional elements NH2.
The alpha form of the neutral polypeptide
chain composed of Alanine, Glycine, and
Phenylalanine appears.
NOTE: You can use the amino acid names preceded
with a ß– to obtain the beta conformation, for example
Hß–Alaß–Glyß–PheOH. To generate the ß
character, type Alt+0223 using the number pad.
The appropriate bonding and dihedral angles
for each amino acid are pre-configured in the
substructure.
Example 3. Polypeptides
Use substructures for building polymers, such as
proteins:
1. Type HAlaGlyPheOH into a text box with no
atoms selected.
The additional H and OH cap the ends of the
polypeptide. If you don’t cap the ends and
automatic rectification is on, Chem3D tries to
fill the open valences, possibly by closing a
ring.
2. Press the Enter key.
Ring closing bonds appear whenever the text in
a text box contains two or more open valences.
TIP: To better view the alpha helix formation, use the
Trackball Tool to reorient the model to an end-on view. For
more information see “Trackball Tool” on page 97.
To change the polypeptide to a zwitterion:
1. Select the Text tool.
2. Click the terminal nitrogen.
A text box appears over the nitrogen atom.
3. Type + and press the Enter key.
The charge is applied to the nitrogen atom. Its
atom type changes and a hydrogen atom is
added.
4. Click the terminal oxygen.
A text box appears over the oxygen atom.
5. Type - in the text box and press the Enter key.
80 •Building and Editing Models CambridgeSoft
Building With The Text Tool