Cleaning

It is possible to clean structures in either 2D or 3D.

Cleaning in 3D can lead to stereoinformation loss (atropisomerism) or creation (chirality not defined in 2D).

Cleaning calculates new coordinates for the atoms. Generating conformers and choosing the favored one is also supported. For more information about molecule cleaning, see Cleaning options.

Clean 2D

The table below lists the Clean 2D actions.

Name

Shortcut

Description

Clean in 2D

Ctrl+2

Calculates new 2D coordinates for the molecule.

Clean and Arrange in 2D

Ctrl+Shift+2

Cleans the molecules and places them in the center of the canvas.

This type of clean uses the set templates for cleaning of the molecules.

Hydrogenize Chiral Center

N/A

Adds explicit hydrogen with a wedge bond to chiral centers which have no terminal atoms as substituents.

Clean in 2D works as Clean and Arrange in 2D if the structure contains an amino acid, a coordinate bond, or a position variation bond.

Clean in 3D

Cleans the molecules in 3D. It is possible to specify the cleaning method. For information about the various cleaning methods, see the 3D Options Tab section of this guide.