Defining Geometric Objects

There are two ways to define geometric objects (centroids, vectors, etc.) when drawing a substructure:

 

Method 1

•	Open up the Geometric Parameters dialogue box by clicking on the ADD 3D mode button or by hitting 3D in the top-level menu and then Add Constraints... in the resulting pull-down menu. The dialogue box can only be opened when there is a substructure in the white drawing area.

•	Select the atoms that are needed to calculate the object by clicking on them with the left-hand mouse button (click again on an atom to deselect).

•	As the number of selected atoms varies, the dialogue box will list the objects that can meaningfully be defined.

•	Hit the appropriate Define button in the dialogue box, e.g. next to the word Centroid to define a centroid.

•	The defined object is listed in the box labelled Defined Objects.In the example below, the centroid of the three ring carbon atoms has been defined:

 

•	An extra step is required for the definition of a dummy point: definition of the distance from the second selected atom at which to create the dummy point (this distance can be negative) (see Dummy Points).

Method 2

•	Go to EDIT mode and select (see Selecting Atoms and Bonds) the atoms required for the object.

•	Hit 3D in the top-level menu and then pick the relevant object in the resulting pull-down menu.

•	The object will be defined immediately except for Dummy Points, where an extra step is required (see above).

Once defined, objects can be used to create geometric parameters, e.g. distances between centroids, or angles between planes (see Defining Geometric Parameters Involving Objects).