User`s guide

2. Building Molecules
• Geometry: Bond lengths and angles are set to ideal values
These steps should be carried out in order, since each step relies on the previous step having
already been completed.
To invoke all three clean-up steps with a single command, choose Clean-Up:
Comprehensive (
).
Before and After Comprehensive Clean-Up
The rules used for cleaning-up structures are based on stable organic molecules. If one is building
a transition state or radical, it is often necessary to manually adjust the molecule during the clean-
up process. Thus, one might build the molecular backbone, choose Clean-Up: Add Hydrogens,
manually add or delete some hydrogen atoms, choose Clean-Up: Hybridization, manually adjust
the hybridization if an atom, and finally choose Clean-Up: Geometry.
To clean up just a portion of the molecule, select the atoms to be cleaned-up, choose Clean-Up:
Selection Only, and then choose the clean-up action that is desired. Atoms that were not selected
will not be affected.
G. Fragments and Fragment Library
Pre-defined structure fragments can be inserted into the editor, saving the effort of manually
creating them and adjusting their geometry.
To insert a fragment, choose the build tool and choose Build: Fragment.... Select the desired
category and fragment, and click OK. Click in the editor to add the chosen fragment.
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