Using Structure CleanUp

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The Structure CleanUp command is used to neaten the appearance of molecules by regularizing bond lengths and angles. Graphic objects such as arrows and aromatic circles are not affected. Use Structure CleanUp to redraw structures that you may have drawn freehand or to neaten structures that you may have imported from another application.

Structure CleanUp may not create the best structure. Most structures have many "clean" forms, a problem that is particularly noticeable with straight-chain alkanes.

If you select only part of a structure when you choose Structure CleanUp, the other atoms and bonds are not be affected.

NOTE: For some compounds, the Structure CleanUp command produces a structure that extends beyond the bounds of the page. To view the entire structure, scale the structure or increase the size of the printed page. For more information, see "Resizing Objects" and "Setting up Pages".

General Rules for Structure CleanUp are:

• The Fixed Length setting in the Drawing Settings dialog determines optimum bond lengths.
• A given ring is redrawn only if all of its bonds are selected.
• Multi-attached atom labels and variable attachment points cannot be cleaned.
• Multi-center bonds cannot be cleaned.
• Structures are rotated so that as many bonds as possible are directed at a multiple of 15 degrees.
• Structure CleanUp preserves stereochemical meaning rather than the precise identity of any wedged or hashed bonds, as shown below.

Using Structure CleanUp:

1. Select the structure or part of the structure you want to clean up with a selection tool.

2. From the Structure menu, choose Structure CleanUp.

NOTE: Structure CleanUp does not position molecules relative to other objects. Overlap may occur.