Moving and Building Molecules

Contents Previous Next

Moving and Building Molecules

General Information

Choose the Edit -> Move/Build... item of the Main Menu to move and/or build molecules (Figure 10).

Figure 10 - The Move/Build Item

A special feature is switched on: you can move a molecule with respect to other structures, select bonds and atoms for rotating its parts and create new molecules. In this case you are now allowed to take some actions such as general selections of atoms, residues and molecules. In order to turn off the Move/Build feature, click on the QUIT button of Builder (Figure 13).

Moving a Molecule or Its Parts

There are two modes for moving a molecule:

· Translate mode. Holding the shift button and the left button of the mouse, you can move the molecules parallel to the screen plane (left, right, up and down) (Figure 11).

Figure 11 - Translate Mode

· Rotate mode. Press the Ctrl button and the Left (Right) button of the mouse to select a bond and rotate a part (Figure 12) (a) or a whole molecule (b).

Figure 12 - Rotate Mode

Building Molecules

You can both build a new molecule and change a given structure by using Builder (Figure 13).

Figure 13 - Builder

This allows you to make the following changes to the structure:

· Build chemical elements (Figure 13)(c), fragments (d), rings (e) and proteins (a). Choose a structure from Builder. After clicking on it, it will appears in the Viewer.

· Create bonds between atoms. Left click on one atom, press Ctrl and middle click on another and then Left click the Create button in the Builder (f). Example: (Figure 14).

Note: This procedure both creates a bond and adds missing hydrogen atoms.

Figure 14 - Creating Bonds

· Add fragments (Figure 13)(d) and rings (e). Left click on an atom then choose a structure from Builder. This structure will be connected to the selected atom. The example below (Figure 15) demonstrates adding CH3 to a selected oxygen atom.

Figure 15 - Adding CH3

· Create multiple bonds. Right click on a bond and then click on the Double bond button in Builder. The single bond will be changed on the double bond.

Note: When changing the bond type, the procedure will automatically change the number of adjusted hydrogen atoms to balance valences.

· Fix the hydrogen atoms in the whole molecule, or add hydrogen atoms to a selected atom (Figure 13)(b). Left click on any atom of the molecule (Figure 16) and then press the fix H button. Hydrogen atoms will be added to all atoms taking into account their bond types. If you would like to add hydrogen atoms only to selected atoms, use the add H button.

Contents Previous Next