Drawing atoms and bonds

with No Comments

Adding an atom

Select an element from the toolbar. In the drawing area click where you want to add the atom. If the option “show missing hydrogen atoms” is set, some atoms (e.g. C, N, O, etc.) will be drawn with hydrogen atoms.

The label of an atom which has one or more bonds can be made invisible by clicking on the atom. By clicking on the invisible atom, the label gets visible again

By double clicking the atom can be edited.

Adding a bond

Select a bond typ from the toolbar. In the drawing area click and drag either on an empty spot or on an existing atom. The red line indicates the direction and lenght of a bond and will lock at certain positions. The locking can be dissable from the menubar (Drawing) or Preferences. You can also connect to existing atoms with a bond.

If the number of bonds is larger as the valence of the connected atoms, a warning will be shown. If you choose to add the bond anyway, the atoms may get charged. The charge can be manually adjusted (Editing atoms).
Adding an atomgroup

Atomgroupds like NO2 can be added by double clicking an existing atom and entering the atomgroup as text.

Leave a Reply