User`s guide

2. Building Molecules
Fragment Library Dialog Box
When adding a fragment to an existing molecule, it is often useful to move the fragment relative
to the molecule. Choose the adjust tool, and select the fragment by dragging a box around it or by
selecting an atom and choosing Adjust: Select Molecule. Then use the Adjust: Rotate
Selection and Adjust: Translate Selection menu items.
The fragment library can be extended by the WebMO system administrator using the Fragment
Manager. Any WebMO job can be imported into the fragment library, making the molecular
structure readily available within the editor.
H. Working With Selections
It is often useful to manipulate a subset of the atoms in the editor, e.g., a portion of a molecule or a
separated fragment.
To create a selection set, one must first invoke the adjust tool with Tools: Adjust (
). Several
methods exist for creating a selection set:
• Click on the first atom and then shift-click on subsequent atoms
• Drag a box around a group of atoms and bonds
• Click on a single atom and choose Adjust: Select Molecule to select all connected
atoms
To clean-up a selection, choose Clean-Up: Selection Only, and then choose the clean-up action
that is desired (Add Hydrogens, Hybridization, Geometry, or Comprehensive). Atoms that
were not selected will not be affected.
To move a selection relative to the rest of the atoms in the editor, use the Adjust: Rotate
Selection and Adjust: Translate Selection menu items. When rotating a selection, dragging the
mouse rotates the selection about the x and y axes (in the plane of the screen), and control-drag
rotates the selection about the z axis (perpendicular to the screen). When translating a selection,
dragging the mouse translates the molecule in the xy plane (plane of the screen), and control-drag
translates the selection along the z axis (perpendicular to the screen). Atoms that were not selected
are not moved.
To duplicate a selection, choose Adjust: Duplicate Selection and then click to insert a copy of
the selection. The copied fragment can be moved relative to the molecule by invoking the adjust
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