Chem3D 8.0 Manual - CambridgeSoft

To find the energy minimum:3. Type the number you want to start at (1 for thisexample).4. Press Enter.The first atom is renumbered as (1).5. Double-click each of the atoms in the order youwant them to be numbered.Each time you double-click an atom to serializeit, the new serial number is one greater than theserial number of the previously serialized atom.6. From the Tools menu, choose Show H’s andLp’s and examine the model using the TrackballTool.The hydrogens appear as far apart as possible.Because you built the structure by using bond tools,you may have distorted bond angles and bondlengths.To correct for distorted angles and lengths:1. From the Edit menu, choose Select All.All of the atoms in the model are selected.2. From the Tools menu, choose Clean UpStructure.To locate an energy minimum for your structurewhich represents a stable conformation of yourmodel, you can use the Minimize Energy commandin the MM2 menu.For more information about energy minimizationsee “Chapter 9: Computation Concepts.”1. From the MM2 menu, choose MinimizeEnergy.2. Leave the values in the dialog box as they areand click Run.After the minimization is complete:1. From the File menu, choose Save.2. Select a directory in which to save the file.3. Type “tut1” in the text box at the bottom of thedialog box.4. Click Save.5. Click the model window to activate it.6. From the File menu, choose Close Window.Tutorial 2: BuildingModels with the TextBuilding ToolThis tutorial illustrates alternative methods to buildmodels using the Text Building Tool.Double-clicking with any other tool selected has thesame effect as single-clicking with the Text Buildingtool. Triple-clicking has the same effect asdouble-clicking with the Text Building tool.NOTE: Element symbols and substructure namesare case sensitive.Open a file:1. From the File menu, choose Open.2. Locate and select the file, “tut1”, that youcreated in the previous tutorial.3. Click Open.Chem3D 8 Chapter 2: Tutorials • 23Tutorial 2: Building Models with the Text Building Tool